create_htan_presentation_states.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 61,
   "id": "a8ff94cb-530c-4be7-8591-f5c487d85cbc",
   "metadata": {},
   "outputs": [],
   "source": [
    "import collections\n",
    "import logging\n",
    "from enum import Enum\n",
    "from pathlib import Path\n",
    "from socket import gethostname\n",
    "from typing import Dict, NamedTuple, Sequence, Tuple\n",
    "\n",
    "import dicomslide as ds\n",
    "import highdicom as hd\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import scipy\n",
    "from sklearn.mixture import GaussianMixture\n",
    "from pydicom.dataset import Dataset\n",
    "from pydicom.sr.coding import Code\n",
    "from dicomweb_client import DICOMwebClient, DICOMClient\n",
    "from dicomweb_client.log import configure_logging\n",
    "from dicomweb_client.ext.gcp.session_utils import (\n",
    "    create_session_from_gcp_credentials\n",
    ")\n",
    "from dicomweb_client.ext.gcp.uri import GoogleCloudHealthcareURL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "0d8760b1-89c3-47e3-9236-a8001444ea2f",
   "metadata": {},
   "outputs": [],
   "source": [
    "logger = logging.getLogger('notebook')\n",
    "configure_logging(0)\n",
    "logger.setLevel(logging.INFO)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "9ef9a34a-358e-4418-b823-664043f25522",
   "metadata": {},
   "outputs": [],
   "source": [
    "url = GoogleCloudHealthcareURL(\n",
    "    project_id='idc-dev-etl',\n",
    "    location='us-central1',\n",
    "    dataset_id='idc',\n",
    "    dicom_store_id='idc_v10_pathology'\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "736f478b-dc90-42a5-bd02-98ad297e86f0",
   "metadata": {},
   "outputs": [],
   "source": [
    "client = DICOMwebClient(\n",
    "    str(url),\n",
    "    session=create_session_from_gcp_credentials()\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "f7ca9b41-dab1-44d2-8f07-9318086d2fd5",
   "metadata": {},
   "outputs": [],
   "source": [
    "COMPONENT_INVESTIGATED = Code('246094008', 'SCT', 'Component investigated')\n",
    "\n",
    "class Colors(Enum):\n",
    "    RED = (230, 43, 0)\n",
    "    GREEN = (0, 225, 0)\n",
    "    BLUE = (25, 84, 255)\n",
    "    CYAN = (25, 225, 255)\n",
    "    YELLOW = (255, 225, 0)\n",
    "    MAGENTA = (255, 43, 255)\n",
    "    WHITE = (225, 225, 225)\n",
    "\n",
    "CHANNEL_GROUPS = (\n",
    "    {\n",
    "        'name': 'PD1-PDL1-CD45-Ecadherin',\n",
    "        'settings': (\n",
    "            (Code(\"19677004\", \"SCT\", \"CD45\"), Colors.BLUE),\n",
    "            (Code(\"C94697\", \"NCIt\", \"PD1\"), Colors.GREEN),\n",
    "            (Code(\"C96024\", \"NCIt\", \"PDL1\"), Colors.RED),\n",
    "            (Code(\"61792\", \"FMA\", \"E-Cadherin\"), Colors.WHITE),\n",
    "        ),\n",
    "    },\n",
    "    {\n",
    "        'name': 'PanCK-Vimentin-CD45-Ki67',\n",
    "        'settings': (\n",
    "            (Code(\"259987000\", \"SCT\", \"Cytokeratin\"), Colors.YELLOW),\n",
    "            (Code(\"75925000\", \"SCT\", \"Vimentin\"), Colors.MAGENTA),\n",
    "            (Code(\"19677004\", \"SCT\", \"CD45\"), Colors.CYAN),\n",
    "            (Code(\"C0208804\", \"UMLS\", \"KI67\"), Colors.WHITE),\n",
    "        )\n",
    "    },\n",
    "    {\n",
    "        'name': 'CD3-CD20-CD68',\n",
    "        'settings': (\n",
    "            (Code(\"24851008\", \"SCT\", \"DNA\"), Colors.WHITE),\n",
    "            (Code(\"44706009\", \"SCT\", \"CD3\"), Colors.CYAN),\n",
    "            (Code(\"82753007\", \"SCT\", \"CD20\"), Colors.MAGENTA),\n",
    "            (Code(\"31001006\", \"SCT\", \"CD68\"), Colors.YELLOW),\n",
    "        )\n",
    "    },\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "2eb9350b-c360-442b-a744-062b9e5092dd",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "def group_images_into_slides(\n",
    "    client: DICOMClient\n",
    ") -> Dict[Tuple[str, str], Tuple[str, str, str, Code]]:\n",
    "    \"\"\"Index slide microscopy images in a DICOM store.\n",
    "    \n",
    "    Parameters\n",
    "    ----------\n",
    "    client: dicomweb_client.DICOMclient\n",
    "        DICOM client\n",
    "        \n",
    "    Returns\n",
    "    -------\n",
    "    Dict[Tuple[str, str], Tuple[str, str, str, Code]]    \n",
    "        Mapping of Study Instance UID and Container Identifier\n",
    "        to Series Instance UID, SOP Instance UID,\n",
    "        Optical Path Identifier and the substance used for\n",
    "        tissue staining\n",
    "    \n",
    "    \"\"\"\n",
    "    # Restrict to HTAN data\n",
    "    found_studies = [\n",
    "        Dataset.from_json(result)\n",
    "        for result\n",
    "        in client.search_for_studies(\n",
    "            search_filters={'PatientName': 'HTA*'},\n",
    "            get_remaining=True,\n",
    "            fuzzymatching=True\n",
    "        )\n",
    "    ]\n",
    "    lut = collections.defaultdict(list)\n",
    "    for study in found_studies:\n",
    "        found_sm_series = [\n",
    "            Dataset.from_json(ds)\n",
    "            for ds in client.search_for_series(\n",
    "                study.StudyInstanceUID,\n",
    "                search_filters={'Modality': 'SM'}\n",
    "            )\n",
    "        ]\n",
    "        for series in found_sm_series:\n",
    "            image_metadata = [\n",
    "                Dataset.from_json(ds)\n",
    "                for ds in client.retrieve_series_metadata(\n",
    "                    study.StudyInstanceUID,\n",
    "                    series.SeriesInstanceUID\n",
    "                )\n",
    "            ]\n",
    "            for image in image_metadata:\n",
    "                if image.SamplesPerPixel > 1:\n",
    "                    continue\n",
    "                key = (\n",
    "                    image.StudyInstanceUID,\n",
    "                    image.ContainerIdentifier,\n",
    "                )\n",
    "                preparation_steps = (\n",
    "                    image\n",
    "                        .SpecimenDescriptionSequence[0]\n",
    "                        .SpecimenPreparationSequence\n",
    "                )\n",
    "                if len(preparation_steps) == 0:\n",
    "                    stain = None\n",
    "                else:\n",
    "                    stains = []\n",
    "                    staining_preparation_step_items = (\n",
    "                        preparation_steps[-1]\n",
    "                            .SpecimenPreparationStepContentItemSequence\n",
    "                    )\n",
    "                    for item in staining_preparation_step_items:\n",
    "                        if item.ValueType != hd.sr.ValueTypeValues.CODE.value:\n",
    "                            continue\n",
    "                        name = hd.sr.utils.get_coded_name(item)\n",
    "                        if name != COMPONENT_INVESTIGATED:\n",
    "                            continue\n",
    "                        value = hd.sr.utils.get_coded_value(item)\n",
    "                        stains.append(value)\n",
    "                    try:\n",
    "                        stain = stains[0]\n",
    "                    except IndexError:\n",
    "                        stain = None\n",
    "                value = (\n",
    "                    image.SeriesInstanceUID,\n",
    "                    image.SOPInstanceUID,\n",
    "                    image.OpticalPathSequence[0].OpticalPathIdentifier,\n",
    "                    stain\n",
    "                )\n",
    "                lut[key].append(value)\n",
    "    return lut"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "32e1af6e-75af-4a03-85ba-867932c2688a",
   "metadata": {},
   "outputs": [],
   "source": [
    "class Channel(NamedTuple):\n",
    "\n",
    "    images: Sequence[Dataset]\n",
    "    voi_range: Tuple[int, int]\n",
    "    color: Tuple[int, int, int]\n",
    "\n",
    "\n",
    "def compute_limit_values(pixel_array: np.ndarray) -> Tuple[int, int]:\n",
    "    \"\"\"Compute minimum and maximum value of the value of interest (VOI) window.\n",
    "\n",
    "    Parameters\n",
    "    ----------\n",
    "    pixel_array: numpy.ndarray\n",
    "        Image region based on which limit values should be computed\n",
    "\n",
    "    Returns\n",
    "    -------\n",
    "    min_value: int\n",
    "        Mininum value (lower limit) of the VOI window\n",
    "    max_value: int\n",
    "        Maximum value (upper limit) of the VOI window\n",
    "\n",
    "    \"\"\"\n",
    "    # Sample pixels with stride along each axis\n",
    "    num_pixels_per_axis = 200\n",
    "    row_stride = np.max([\n",
    "        1,\n",
    "        int(np.floor(pixel_array.shape[0] / num_pixels_per_axis))\n",
    "    ])\n",
    "    col_stride = np.max([\n",
    "        1,\n",
    "        int(np.floor(pixel_array.shape[1] / num_pixels_per_axis))\n",
    "    ])\n",
    "    row_indices = np.arange(0, pixel_array.shape[0], row_stride)\n",
    "    col_indices = np.arange(0, pixel_array.shape[1], col_stride)\n",
    "    # Slice one axis at a time to save memory\n",
    "    rows = pixel_array[row_indices]\n",
    "    values = rows[:, col_indices]\n",
    "\n",
    "    # Log transform values\n",
    "    log_values = np.log(values[values > 0])\n",
    "\n",
    "    # Train model on log transformed pixel values\n",
    "    model = GaussianMixture(3, max_iter=1000, tol=1e-6)\n",
    "    model.fit(log_values.reshape((-1, 1)))\n",
    "\n",
    "    # Get the parameters of the top two Gaussian distributions, which are\n",
    "    # assumed to be tissue autoflorescence and stain fluorescence signal.\n",
    "    # Ignore the Gaussian distribution with the lowest mean, which is assumed\n",
    "    # to be camera background.\n",
    "    means = model.means_[:, 0]\n",
    "    _, index1, index2 = np.argsort(means)\n",
    "    mean1, mean2 = means[[index1, index2]]\n",
    "    std1, std2 = model.covariances_[[index1, index2], 0, 0] ** 0.5\n",
    "    weights1, weights2 = model.weights_[[index1, index2]]\n",
    "\n",
    "    # Choose upper limit value two standard deviations away from the mean of\n",
    "    # the Gaussian that represents the stain fluorescence signal.\n",
    "    lmax = mean2 + 2 * std2\n",
    "\n",
    "    # Choose lower limit value in between the two Gaussians that represent the\n",
    "    # tissue autoflorescence and stain fluorescence signal.\n",
    "    x = np.linspace(mean1, mean2, 50)\n",
    "    y1 = scipy.stats.norm(mean1, std1).pdf(x) * weights1\n",
    "    y2 = scipy.stats.norm(mean2, std2).pdf(x) * weights2\n",
    "    lmin = x[np.argmin(np.abs(y1 - y2))]\n",
    "    if lmin >= mean2:\n",
    "        lmin = mean2 - 2 * std2\n",
    "\n",
    "    # Undo the log transformation to get the min and max value of interst (VOI)\n",
    "    voi_min = np.exp(lmin)\n",
    "    voi_max = np.exp(lmax)\n",
    "\n",
    "    # Ensure that min and max values lie within the pixel values.\n",
    "    voi_min = max(voi_min, values.min(), 0)\n",
    "    voi_max = min(voi_max, values.max())\n",
    "\n",
    "    return (voi_min, voi_max)\n",
    "\n",
    "\n",
    "def _create_palette_color_lut_transformation(\n",
    "    color: Tuple[int, int, int]\n",
    ") -> hd.PaletteColorLUTTransformation:\n",
    "    bits_per_entry = 16\n",
    "    high_value = 255\n",
    "    dtype = np.dtype(f'uint{bits_per_entry}')\n",
    "\n",
    "    red_segment_values = [\n",
    "        0, 1, 0,\n",
    "        1, high_value, color[0],\n",
    "    ]\n",
    "    green_segment_values = [\n",
    "        0, 1, 0,\n",
    "        1, high_value, color[1],\n",
    "    ]\n",
    "    blue_segment_values = [\n",
    "        0, 1, 0,\n",
    "        1, high_value, color[2],\n",
    "    ]\n",
    "\n",
    "    transformation = hd.PaletteColorLUTTransformation(\n",
    "        red_lut=hd.SegmentedPaletteColorLUT(\n",
    "            first_mapped_value=0,\n",
    "            segmented_lut_data=np.array(red_segment_values, dtype=dtype),\n",
    "            color='red'\n",
    "        ),\n",
    "        green_lut=hd.SegmentedPaletteColorLUT(\n",
    "            first_mapped_value=0,\n",
    "            segmented_lut_data=np.array(green_segment_values, dtype=dtype),\n",
    "            color='green'\n",
    "        ),\n",
    "        blue_lut=hd.SegmentedPaletteColorLUT(\n",
    "            first_mapped_value=0,\n",
    "            segmented_lut_data=np.array(blue_segment_values, dtype=dtype),\n",
    "            color='blue'\n",
    "        )\n",
    "    )\n",
    "    return transformation\n",
    "\n",
    "\n",
    "def create_presentation_state(\n",
    "    channels: Sequence[Channel],\n",
    "    series_instance_uid: str,\n",
    "    series_number: int,\n",
    "    instance_number: int\n",
    ") -> hd.pr.AdvancedBlendingPresentationState:\n",
    "    \"\"\"Create presentation state instance for data visualization.\n",
    "\n",
    "    Parameters\n",
    "    ----------\n",
    "    channels: Sequence[Tuple[Sequence[pydicom.Dataset], Tuple[int, int], Tuple[int, int, int]]]\n",
    "        Information about channels (optical paths) that should be visualized\n",
    "    series_instance_uid: str\n",
    "        DICOM Series Instance UID that should be assigned to created instance\n",
    "    series_number: int\n",
    "        Number of the series in the parent study\n",
    "    instance_number: int\n",
    "        Number of the created instance in the series\n",
    "\n",
    "    Returns\n",
    "    -------\n",
    "    highdicom.pr.AdvancedBlendingPresentationState\n",
    "        DICOM Advanced Blending Presentation State instance\n",
    "\n",
    "    \"\"\"  # noqa: E501\n",
    "    referenced_images = []\n",
    "    blending_configurations = []\n",
    "    blending_display_inputs = []\n",
    "    channel_descriptions = []\n",
    "    for i, ch in enumerate(channels):\n",
    "        voi_lut_transformation = hd.pr.SoftcopyVOILUTTransformation(\n",
    "            window_center=float(np.mean(ch.voi_range)),\n",
    "            window_width=float(np.abs(np.diff(ch.voi_range))),\n",
    "        )\n",
    "        palette_color_lut_transformation = \\\n",
    "            _create_palette_color_lut_transformation(ch.color)\n",
    "\n",
    "        blending_input_number = i + 1  # one-based index\n",
    "        configuration = hd.pr.AdvancedBlending(\n",
    "            referenced_images=ch.images,\n",
    "            blending_input_number=blending_input_number,\n",
    "            voi_lut_transformations=[voi_lut_transformation],\n",
    "            palette_color_lut_transformation=palette_color_lut_transformation\n",
    "        )\n",
    "        display_input = hd.pr.BlendingDisplayInput(blending_input_number)\n",
    "\n",
    "        description = ch.images[0].OpticalPathSequence[0].OpticalPathDescription\n",
    "        channel_descriptions.append(description)\n",
    "        referenced_images.extend(ch.images)\n",
    "        blending_configurations.append(configuration)\n",
    "        blending_display_inputs.append(display_input)\n",
    "\n",
    "    blending_display = hd.pr.BlendingDisplay(\n",
    "        blending_mode=hd.pr.BlendingModeValues.EQUAL,\n",
    "        blending_display_inputs=blending_display_inputs\n",
    "    )\n",
    "\n",
    "    return hd.pr.AdvancedBlendingPresentationState(\n",
    "        referenced_images=referenced_images,\n",
    "        blending=blending_configurations,\n",
    "        blending_display=[blending_display],\n",
    "        series_instance_uid=series_instance_uid,\n",
    "        series_number=series_number,\n",
    "        sop_instance_uid=hd.UID(),\n",
    "        instance_number=instance_number,\n",
    "        manufacturer='Herrmann Lab',\n",
    "        manufacturer_model_name='timux',\n",
    "        software_versions='0.1.0',\n",
    "        device_serial_number=gethostname(),\n",
    "        content_label='MULTIPLEXED_IF',\n",
    "        content_description='-'.join(channel_descriptions),\n",
    "        institution_name='Massachusetts General Hospital',\n",
    "        institutional_department_name='Pathology',\n",
    "        content_creator_name='Herrmann^Markus^D'\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "7659fac5-2e8a-491e-a357-4b23d3f91500",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2022-07-02 15:12:08 | WARNING  | dicomweb_client.web                      | empty response\n"
     ]
    }
   ],
   "source": [
    "slide_info = group_images_into_slides(client)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "ee709709-0174-42bb-89ab-993c58a1c838",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "compound_mapping = collections.defaultdict(list)\n",
    "for (study_instance_uid, container_id), values in slide_info.items():\n",
    "    for v in values:\n",
    "        compound = v[-1]\n",
    "        if compound is not None:\n",
    "            compound_mapping[compound].append((study_instance_uid, container_id))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "78c0883c-ca17-4548-bf1e-7af2d27ce0c9",
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Code(\"24851008\", \"SCT\", \"DNA\")\n",
      "101\n",
      "--\n",
      "Code(\"146671000146103\", \"SCT\", \"Rat protein\")\n",
      "16\n",
      "--\n",
      "Code(\"C104064\", \"NCIt\", \"CD163\")\n",
      "109\n",
      "--\n",
      "Code(\"146321000146106\", \"SCT\", \"Rabbit protein\")\n",
      "16\n",
      "--\n",
      "Code(\"C104394\", \"NCIt\", \"FOXP3\")\n",
      "112\n",
      "--\n",
      "Code(\"C96024\", \"NCIt\", \"PDL1\")\n",
      "122\n",
      "--\n",
      "Code(\"61792\", \"FMA\", \"E-Cadherin\")\n",
      "101\n",
      "--\n",
      "Code(\"75925000\", \"SCT\", \"Vimentin\")\n",
      "101\n",
      "--\n",
      "Code(\"C25899\", \"NCIt\", \"CDX2\")\n",
      "16\n",
      "--\n",
      "Code(\"C17307\", \"NCIt\", \"Lamin\")\n",
      "16\n",
      "--\n",
      "Code(\"83475004\", \"SCT\", \"Desmin\")\n",
      "16\n",
      "--\n",
      "Code(\"4167003\", \"SCT\", \"CD31\")\n",
      "101\n",
      "--\n",
      "Code(\"146681000146101\", \"SCT\", \"Mouse protein\")\n",
      "16\n",
      "--\n",
      "Code(\"C17323\", \"NCIt\", \"PCNA\")\n",
      "23\n",
      "--\n",
      "Code(\"C0208804\", \"UMLS\", \"KI67\")\n",
      "116\n",
      "--\n",
      "Code(\"89048009\", \"SCT\", \"Collagen type IV\")\n",
      "20\n",
      "--\n",
      "Code(\"259987000\", \"SCT\", \"Cytokeratin\")\n",
      "100\n",
      "--\n",
      "Code(\"LP35599-7\", \"LN\", \"Smooth Muscle Actin\")\n",
      "101\n",
      "--\n",
      "Code(\"24655002\", \"SCT\", \"CD4\")\n",
      "118\n",
      "--\n",
      "Code(\"19677004\", \"SCT\", \"CD45\")\n",
      "142\n",
      "--\n",
      "Code(\"C94697\", \"NCIt\", \"PD1\")\n",
      "129\n",
      "--\n",
      "Code(\"82753007\", \"SCT\", \"CD20\")\n",
      "116\n",
      "--\n",
      "Code(\"31001006\", \"SCT\", \"CD68\")\n",
      "133\n",
      "--\n",
      "Code(\"C104109\", \"NCIt\", \"CD8a\")\n",
      "94\n",
      "--\n",
      "Code(\"5404007\", \"SCT\", \"CD45RA\")\n",
      "41\n",
      "--\n",
      "Code(\"130636000\", \"SCT\", \"Granzyme B\")\n",
      "96\n",
      "--\n",
      "Code(\"58520002\", \"SCT\", \"Collagen type I\")\n",
      "82\n",
      "--\n",
      "Code(\"44706009\", \"SCT\", \"CD3\")\n",
      "113\n",
      "--\n",
      "Code(\"C45438\", \"NCIt\", \"PD-L2\")\n",
      "41\n",
      "--\n",
      "Code(\"86076000\", \"SCT\", \"CD45RO\")\n",
      "78\n",
      "--\n",
      "Code(\"C16692\", \"NCIt\", \"HLA-DR\")\n",
      "78\n",
      "--\n",
      "Code(\"C16685\", \"NCIt\", \"Histone H3\")\n",
      "85\n",
      "--\n",
      "Code(\"27130004\", \"SCT\", \"CD11b\")\n",
      "80\n",
      "--\n",
      "Code(\"C104623\", \"NCIt\", \"LAG-3\")\n",
      "78\n",
      "--\n",
      "Code(\"46959001\", \"SCT\", \"CD11c\")\n",
      "80\n",
      "--\n",
      "Code(\"62998003\", \"SCT\", \"CD74\")\n",
      "37\n",
      "--\n",
      "Code(\"84640000\", \"SCT\", \"Nucleus\")\n",
      "41\n",
      "--\n",
      "Code(\"C17392\", \"NCIt\", \"CSF1R\")\n",
      "16\n",
      "--\n",
      "Code(\"C18489\", \"NCIt\", \"CD209\")\n",
      "13\n",
      "--\n",
      "Code(\"8164002\", \"SCT\", \"CD66B\")\n",
      "15\n",
      "--\n",
      "Code(\"C0142251\", \"UMLS\", \"CD208\")\n",
      "15\n",
      "--\n",
      "Code(\"C20705\", \"NCIt\", \"HLA Class II\")\n",
      "15\n",
      "--\n",
      "Code(\"130616001\", \"SCT\", \"Tryptase\")\n",
      "13\n",
      "--\n",
      "Code(\"C106314\", \"NCIt\", \"RORGT\")\n",
      "13\n",
      "--\n",
      "Code(\"C129059\", \"NCIt\", \"NKP46\")\n",
      "9\n",
      "--\n",
      "Code(\"54237000\", \"SCT\", \"CD8\")\n",
      "35\n",
      "--\n",
      "Code(\"C104249\", \"NCIt\", \"TBET\")\n",
      "22\n",
      "--\n",
      "Code(\"C75494\", \"NCIt\", \"GATA3\")\n",
      "13\n",
      "--\n",
      "Code(\"C102928\", \"NCIt\", \"EOMES\")\n",
      "15\n",
      "--\n",
      "Code(\"C79782\", \"NCIt\", \"IDO\")\n",
      "7\n",
      "--\n",
      "Code(\"42891003\", \"SCT\", \"CD56\")\n",
      "4\n",
      "--\n",
      "Code(\"C20512\", \"NCIt\", \"Interleukin-10\")\n",
      "6\n",
      "--\n",
      "Code(\"C94803\", \"NCIt\", \"Inducible T-Cell Costimulator\")\n",
      "6\n",
      "--\n",
      "Code(\"C101577\", \"NCIt\", \"CCR2\")\n",
      "2\n",
      "--\n",
      "Code(\"13925004\", \"SCT\", \"DNA, Double-Stranded\")\n",
      "2\n",
      "--\n",
      "Code(\"C20706\", \"NCIt\", \"HLA Class I\")\n",
      "2\n",
      "--\n",
      "Code(\"86960007\", \"SCT\", \"Epidermal growth factor-urogastrone receptor\")\n",
      "3\n",
      "--\n",
      "Code(\"LP37239-8\", \"LN\", \"BCL2 Antigen\")\n",
      "3\n",
      "--\n",
      "Code(\"D053537\", \"MSH\", \"Cytokeratin 17\")\n",
      "7\n",
      "--\n",
      "Code(\"D053547\", \"MSH\", \"Cytokeratin 14\")\n",
      "7\n",
      "--\n",
      "Code(\"C117468\", \"MSH\", \"PDPN protein\")\n",
      "7\n",
      "--\n",
      "Code(\"D053552\", \"MSH\", \"Cytokeratin 7\")\n",
      "7\n",
      "--\n",
      "Code(\"D053533\", \"MSH\", \"Cytokeratin 8\")\n",
      "3\n",
      "--\n",
      "Code(\"LP173628-1\", \"LN\", \"Phospho-S6 ribosomal protein\")\n",
      "3\n",
      "--\n",
      "Code(\"C116018\", \"NCIt\", \"Histone H3 Lysine 28\")\n",
      "3\n",
      "--\n",
      "Code(\"709132000\", \"SCT\", \"Cytokeratin 19\")\n",
      "7\n",
      "--\n",
      "Code(\"C107427\", \"NCIt\", \"Histone H3 Lysine 4\")\n",
      "3\n",
      "--\n",
      "Code(\"D016160\", \"MSH\", \"Retinoblastoma Protein\")\n",
      "3\n",
      "--\n",
      "Code(\"D051272\", \"MSH\", \"Glucose Transporter Type 1\")\n",
      "3\n",
      "--\n",
      "Code(\"D003576\", \"MSH\", \"Cytochrome c Oxidase Subunit IV\")\n",
      "3\n",
      "--\n",
      "Code(\"C17971\", \"NCIt\", \"Caveolin-1\")\n",
      "3\n",
      "--\n",
      "Code(\"C468783\", \"MSH\", \"gamma-H2AX protein\")\n",
      "3\n",
      "--\n",
      "Code(\"C495153\", \"MSH\", \"RAD51 protein\")\n",
      "3\n",
      "--\n",
      "Code(\"D053555\", \"MSH\", \"Cytokeratin 5\")\n",
      "7\n",
      "--\n",
      "Code(\"C17319\", \"NCIt\", \"ERBB2\")\n",
      "7\n",
      "--\n",
      "Code(\"C17069\", \"NCIt\", \"Estrogen Receptor\")\n",
      "7\n",
      "--\n",
      "Code(\"C17063\", \"NCIt\", \"Androgen Receptor\")\n",
      "4\n",
      "--\n",
      "Code(\"C17075\", \"NCIt\", \"Progesterone Receptor\")\n",
      "3\n",
      "--\n",
      "Code(\"C17772\", \"NCIt\", \"CD44\")\n",
      "7\n",
      "--\n",
      "Code(\"C478221\", \"MSH\", \"LAMB1 protein\")\n",
      "1\n",
      "--\n"
     ]
    }
   ],
   "source": [
    "for compound, identifiers in compound_mapping.items():\n",
    "    print(f'Code(\"{compound.value}\", \"{compound.scheme_designator}\", \"{compound.meaning}\")')\n",
    "    print(len(set(identifiers)))\n",
    "    print('--')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "id": "c4e1cc30-b0d6-4369-b5b8-fbaae2ce2b54",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "search for slides of study \"2.25.67204616595610313210404611407915801307\" and container \"HTA7_989_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_989_1000 8e9ebac17f10f1a287a02f3ac01af3778fbe6e3e113a21d0b8e8e5eabdf50901>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_989_1000\" of study \"2.25.67204616595610313210404611407915801307\" \n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1108\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1108 fa4e3c9570dc3eef1050fe30babf42289baecb42084631581d37311f62c7a757>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1112\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1112 37e36afe13f09ab17b3ee82f92f1af6429c7b53efe4d291c45ab95f2a3a3b862>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1106\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1106 534f50ee30950a170d62821445c0c9e9ffba7bfe14e250a8a586ebc92723d7b6>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1107\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1107 5adffc20a0f682784fb653ce616a78e15cd20b4d28acf0b281662560efe86e9a>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1104\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1104 1b66d0856c55f0d8f2b6ab24042aecdd842f7c9bf4f763c56e22ab68dc497a4b>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1102 5f18173590cbf23ef62604f8879315e09513035c33bed038f558b966d3bf1c50>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1110\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1110 34f705015400762e5cc7cf0585df792ea14e839726c988c35c8f2df8ba7caa06>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1103 0abe11c6c7bb3e9b9b36f22b25e32dbc95d67651ea91261b785ff04f92581e3a>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.289188443974026654725116153923555879592\" and container \"HTA12_3_1111\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_3_1111 6b20422b65b01fe7805f0ef144014f0f85b574078b59d571a9d5045f23b4826b>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1103 359229694861709c25b992ea50d2e8d5b4832c104a8c64e4d3ad088c40ffa7b6>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1115\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1115 b34dda0a2e2b9f9b37218d4bbae66abef15f26b0bb130e6b797a5661a1589697>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1105\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1105 ff1ade3ca53a4de807daa6e7c9843aaf760603a9e867f6fcf8009c91199a8e04>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1111\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1111 acd2bb991422c9e1d025fada77e087febac9e02dc4adcc94e0c0a5382ebd5756>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1102 f67ffd32559a5a40c7d95c242805bbe0e68b8953610abbb7453f5c85743a73f2>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1116\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1116 160637e62c24cdbd5ff2c8baf9272666bc3692112cd2830e76667821b384d0ea>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1108\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1108 eddfddac927033c611e9f0458aa3df8c6bd3a8797fc6adabece055072af2d8c9>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1107\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1107 61fe2d8ed6e2fb1ec256bd15a767db433cd4b14f4c7af42a2bdd05eef3a20b06>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1113\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1113 8d898dd76ca60220204b6ba66d85024afb113b2fb296ee8c97910606c8bc9477>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1112\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1112 6901d0933a185bfba36d93fd6852a71bd5eb5231b5946f262c7bc722388fec8b>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1109\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1109 f967369449945ea5bfc636fc86293cdcb79e135181e4329e8986a972bb0f2cf0>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.305755249420617670925805518669597959172\" and container \"HTA12_4_1104\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_4_1104 db7d40b7f804eeb96d985c66c5f5ae1d6263deae53327d8fd07adf06158286d3>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.63504200218356539417558724289824234398\" and container \"HTA7_931_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_931_1000 3255cd461ede74eb1ece154ea0bbce01f6bd80bc635c6f69a6da0787d98ae2e1>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_931_1000\" of study \"2.25.63504200218356539417558724289824234398\" \n",
      "search for slides of study \"2.25.253443077977640338251305809014416841249\" and container \"HTA12_16_1108\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_16_1108 12759753b358d4e82b6eb37a0a8a6db259f3cb8f41cfaca8d201b0a7df8f78ac>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.253443077977640338251305809014416841249\" and container \"HTA12_16_1111\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_16_1111 541e881dd67aa6b69e3ec9a4f6a1a2601ef476a157b3dc65d86baa22d566cd2a>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.253443077977640338251305809014416841249\" and container \"HTA12_16_1107\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_16_1107 0274af8c0c6ffcad23d98b592b8babaeb309ce7ee7601c081a248c05ec3f9563>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.253443077977640338251305809014416841249\" and container \"HTA12_16_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_16_1102 0ddbd8caaeb87151da77ed15eb1d0e6c3985212cc470fc911be07519d1c5ca75>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.253443077977640338251305809014416841249\" and container \"HTA12_16_1110\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_16_1110 a6c4063fe5f2f15b170149a482879550cecda98becf1cf57b5bdce452ce3fd3c>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.253443077977640338251305809014416841249\" and container \"HTA12_16_1106\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_16_1106 34866ab10a46d98d9c880641e40ae94584b8703a042ee60ac812c611f3348342>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.253443077977640338251305809014416841249\" and container \"HTA12_16_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_16_1103 f474339b29c5ceebbdcfb70990967258fd877716f9745b7190081e6c638e693e>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.253443077977640338251305809014416841249\" and container \"HTA12_16_1109\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_16_1109 7694cad612799c2b5c545653abd3a501d9ec642f715ee2d1525f40f01a0838e4>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.332948525917882045731716820411285694886\" and container \"HTA7_932_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_932_1000 d825aece9ea51115912b3c421b5840d6dc4849281a8ba7c9ea3d97eff4bb1f96>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_932_1000\" of study \"2.25.332948525917882045731716820411285694886\" \n",
      "search for slides of study \"2.25.282637067979823650115729450350003058980\" and container \"HTA12_15_1106\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_15_1106 aa37f1dbf52cab819cfab9329364da443458d2f89af03738d33ca238c186979b>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.282637067979823650115729450350003058980\" and container \"HTA12_15_1107\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_15_1107 94e52d46e3a7dfe01d154be24f0524c6c43f7964caa9a788e837d3ffcf53a9f3>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.282637067979823650115729450350003058980\" and container \"HTA12_15_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_15_1102 cab49462d7abd66ac5f3f24f0b2f4830f0e9886b22607181ba10d51c57a6d6cd>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.282637067979823650115729450350003058980\" and container \"HTA12_15_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_15_1103 434118ec300c8d748c563c60d9f7cd7abc848f5b5b890d9fe48cb861a1c4f62f>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.282637067979823650115729450350003058980\" and container \"HTA12_15_1105\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_15_1105 a092037e9e334a424f2d09999d16b792f2ba6f0d5f4e5d365a34c4441400a6a4>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.282637067979823650115729450350003058980\" and container \"HTA12_15_1110\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_15_1110 48fe0325b33b83eb86e7611c859e30f9c9fec4ccb94aabe1462847499af26be9>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.282637067979823650115729450350003058980\" and container \"HTA12_15_1109\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_15_1109 122bc17bb0adc1c8beb02f1f15d29530ac18d446b45be83e42797f9e4969ed28>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.66963730400918147916879305140687405342\" and container \"HTA12_11_1108\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_11_1108 bfa911f0b88e0ef52ac96a4afa1845b56f3b75f954c0675cc78fc227fddb498c>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.66963730400918147916879305140687405342\" and container \"HTA12_11_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_11_1102 4c9577fdbfdc96ab9739c80e97527c27438b478e8b48d534d08e82b7d72d8eb3>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.66963730400918147916879305140687405342\" and container \"HTA12_11_1110\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_11_1110 4d2954677fea171ed7472ec476a606be07d63237df10540a095888ffd278dff0>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.66963730400918147916879305140687405342\" and container \"HTA12_11_1105\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_11_1105 1b8ae31bba9201bed8e59cb70eea618f1d4e3ac7a5648af757d6df92931792e3>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.66963730400918147916879305140687405342\" and container \"HTA12_11_1106\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_11_1106 84066f01f3e97508459a562c3694144d101e3ba08d2003a699722289af84cbd3>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.66963730400918147916879305140687405342\" and container \"HTA12_11_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_11_1103 3af469abec6a5c40f63f5a6d056ded7a497fdb0dfa71123f1c8941ef75d3f59f>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.66963730400918147916879305140687405342\" and container \"HTA12_11_1109\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_11_1109 d1fc45285dd082f711fcf736bb7e286ecf319c662acce1bdf811545b88045b8f>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.162372274059988388010059723761949093273\" and container \"HTA12_1_1109\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_1_1109 8b202e688a01072f6759ed060023149bff9bfcff80e0b50b143ed5ec7ec7a128>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.162372274059988388010059723761949093273\" and container \"HTA12_1_1110\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_1_1110 6ce9ca9ffe114a6f86b3643b0822e486a359c29ca1fa494179e568758a94612a>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.162372274059988388010059723761949093273\" and container \"HTA12_1_1107\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_1_1107 0e22fcfcfaba4e5c3802567c9b4f4b54bcd8de079a826b968a41cf5e5e7838c5>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.162372274059988388010059723761949093273\" and container \"HTA12_1_1108\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_1_1108 fbb98746333af10397a0451e5ac9d308bee86a5db1a61c27362fac29030d6a76>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.162372274059988388010059723761949093273\" and container \"HTA12_1_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_1_1103 85d2effc01cf90405a98b49593335c52f0fdc3583f55763494026fbcd08c3d53>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.162372274059988388010059723761949093273\" and container \"HTA12_1_1111\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_1_1111 2f68801187346e3cf67aa77d29a1a5a9894c388147122003a4d6823798fd314b>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.162372274059988388010059723761949093273\" and container \"HTA12_1_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_1_1102 98fd026f0d7fef3184d138839a4aeba21b57cc91c00f4a2e8dce2c8c8d703d82>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.162372274059988388010059723761949093273\" and container \"HTA12_1_1104\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_1_1104 f2d6cf39aa3c31d8c45abbed330b388cc2ea9dd847c1634769f37153732332b4>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.93749216439228361118017742627453453196\" and container \"HTA7_926_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_926_1000 fa6dab3b99045ee2f5d91b47a3f546b5c84042e0a7bafb5b51b35e6c6181e3f9>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_926_1000\" of study \"2.25.93749216439228361118017742627453453196\" \n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1103 efcfd3cb06f4c9ceb8693c21cbb7b2528c90cccefbaf8f6854b028751591501e>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1112\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1112 3b3becf20658050ae6987f27f129f8b570e2de8022666241da7d1cb68cb0da4b>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1104\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1104 5f7f10388637d97d570201f5a1f815eeb25447b47da1200361ae54681ed3a0d8>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1113\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1113 0c70d42fb944184836d77b1d65d09ab09ce1506233723be0d77e0cbac1d75339>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1107\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1107 8cc2714dc395b720fe5503ec23c011f2a7fb7729a81a9e00b72602c0592d62a8>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1106\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1106 86331bcf0234ca7556f568bfac2cf41a0b456cec3a52983466858bc720065d51>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1110\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1110 430c69ea971655c52570eda8eb84790f815231b6fbf8ec7ebc8e0dfac680cd57>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1109\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1109 f807cc13928be23089d2682687cd478088aee7cd297bc4e58c6621acc0401ebe>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.38649134330414220812979591492650088495\" and container \"HTA12_9_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_9_1102 e6d1d092067c636bd553bf073786ac88ff49400e75a03d93060c07df701d664d>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.14542022415536418286893333022896470177\" and container \"HTA7_966_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_966_1000 6829fa8606dad1fd26f1ea5dd9baf9af392740533ca11bf73cc045b145dc0fb0>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_966_1000\" of study \"2.25.14542022415536418286893333022896470177\" \n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1113\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1113 badc8fc4f7ed22e3bea22743c0e22568f43a251c25dbe2e33efa78de24993023>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1106\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1106 aebbce683c394ad2e3265ec014acb76a91a7879149842ce3c7a76f64508caa81>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1112\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1112 cbb0d24072c3780aac69ba67a2aaa6e4d662e117fc3e54192e4d6b003d030f73>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1115\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1115 cc228d22861be74ad0539820a1ee33019f1f29dc48d5bc83c8b0812fab92035a>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1110\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1110 04825286ee581206a60e577e2058f9957f2aeb39f2d7af6731e301d79c43dddd>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1104\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1104 9dee12a0bea39e5971d84b5404eb591bc70cc6727c24912ba786ceaa78cb6bf5>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1102 65078a3c626e4e518559e98d0f8ff27113a7325130236c47c5e0cfc3bdfc0f80>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1114\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1114 0ddc7b11d031de04c75c762d3ec48ca67b833fa87c618c628f9f442101f51b67>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1103 736066c3e637715c87297ceb0805bc935189e8f24fbb8b412b6ed3290609f7f6>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1109\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1109 0f0cfc065e583ad00b76f02c64cf322a8bb8ddd4a3e4e03d1fd56833da6121f9>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1108\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1108 9d6d48178d1796b3b9b4e6de059a5b1ae268d5f4a88c0c4bffeb24fd876ec24b>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.168515530826293760290828161861507472012\" and container \"HTA12_2_1107\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_2_1107 aa825943548d020c97fd95d920e99bead793fc048b48b07498383847b242931f>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.12616158998399217132499508662048718824\" and container \"HTA7_963_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_963_1000 b769653463291bc365f6c49a70a4cf6607fb5d24b1215709cced20adb5fd71f5>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_963_1000\" of study \"2.25.12616158998399217132499508662048718824\" \n",
      "search for slides of study \"2.25.110940496032974123445604819863673717982\" and container \"HTA7_925_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_925_1000 db2e5a2e79b7625ade8e103864298e6fb3b464ff04b4f548b02fa905a8039713>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_925_1000\" of study \"2.25.110940496032974123445604819863673717982\" \n",
      "search for slides of study \"2.25.322763956086448848651654481429424487892\" and container \"HTA7_982_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_982_1000 8dfacd11ae551020fd4179eb2af3296e2a799602682071bc2f5e98ec9284c79e>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_982_1000\" of study \"2.25.322763956086448848651654481429424487892\" \n",
      "search for slides of study \"2.25.117883364358159671221262672841070158229\" and container \"HTA7_934_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_934_1000 e4fcc8af88b71f7b0aff95d4a460c2dc77785063be440d0299a364208b7c0f21>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_934_1000\" of study \"2.25.117883364358159671221262672841070158229\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19363\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19363 f6e17ee2496d4168d996b3be55d0f0d863b35409af51ddb235f0fe5c4a80a1ea>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19363\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19396\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19396 994df41b2f619e03bdcb90cae0a17e8c70e8254f7ddca3bd68acdbf64179b78f>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19396\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19380\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19380 579f24ae7480d9b7ccb0db4d269e45fee93715cf3d1337d8b075631407fbc481>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19380\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19405\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19405 fc7d46ea87c0275dc3aacfcd0952b72e07b33fd05bce700c3c79683863d94e63>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19405\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19405\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19405\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19405\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19405\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19405\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19405\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19375\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19375 415edb026fcd0a71f133549bcc33efc6919408a6972ed7cb8467368b31683c13>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"PDL1\" for slide \"HTA9_1_19375\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19375\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19375\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19375\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19375\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19375\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19358\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19358 3b917bc09f24b949f5d7200194719a93a754da02c236679e9ceefdb25c3886d6>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19358\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19358\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19358\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19358\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19358\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19358\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19358\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19360\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19360 e37924660f7a8ef335304be525ba3896dee4b981d6c41e8c33cfd4980a683833>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PDL1\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19360\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19379\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19379 82cc2b2b6fd51ca3c1ad2c363921c77fbe8685ffd49117b6f899932115f11701>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PDL1\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19379\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19366\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19366 daed5743342027555a2db97ec96e5e38fa0025da91a2dbad65493fd6fbdc41c6>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PDL1\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19366\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19350\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19350 a222c20c0b2222f9df00fea0bda10804ea0efea50829026568e16c9d4ebc3296>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PDL1\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19350\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19399\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19399 c90176e0091245b10a18cb1335f877205f978defb0f0de2d36111873c96f6ea8>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19399\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19399\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19399\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19399\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19399\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19399\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19399\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19364\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19364 ff8ca0e32095ddf418c0bb71c7298c149e7b22b10b5a84b21f0c243a5e56bcb7>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"PDL1\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD45\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19364\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19388\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19388 85b59eeb7b6eab40e0b20e38db14842795f42755f8e37e9801724c3410b30f39>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"PD1\" for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19388\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19403\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19403 3b07eff1e933a36a6837767f2c7a431d1fabca2b96c2b4bc8866a2a3d1d4c083>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"PDL1\" for slide \"HTA9_1_19403\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19403\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19403\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19403\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19403\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19403\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19390\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19390 e5cf4ce6b00618bc3ffbe8a21fff553930e2b28e48a8f9f22af66d8f130352ba>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19390\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19390\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19390\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19390\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19390\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19390\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19390\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19369\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19369 5b4959ebd7990bbba04e58ce217c4b3b6caa0db54672320b63a9a54bc5e1e6a2>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19369\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19369\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19369\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19369\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "WARNING - skip presentation state for slide \"HTA9_1_19369\" of study \"2.25.56219147941526607962658668060030231728\" because of lack of matching optical paths\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19369\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD68\" for slide \"HTA9_1_19369\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19378\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19378 54c7a63c2ae6db72ddd09a71900999275e2a355348a0cb5a841a28fd1afeef5a>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19378\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19378\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"KI67\" for slide \"HTA9_1_19378\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19378\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19383\"\n",
      "ERROR - skip slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19383\": Pyramids for different channels and focal planes must have the same structure, i.e., the same number of levels as well as the same dimensions and downsampling factors per level.\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA9_1_19378 54c7a63c2ae6db72ddd09a71900999275e2a355348a0cb5a841a28fd1afeef5a>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "ERROR - could not find an optical path for stain \"PDL1\" for slide \"HTA9_1_19383\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"E-Cadherin\" for slide \"HTA9_1_19383\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "ERROR - could not find an optical path for stain \"Cytokeratin\" for slide \"HTA9_1_19383\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"Vimentin\" for slide \"HTA9_1_19383\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"DNA\" for slide \"HTA9_1_19383\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "ERROR - could not find an optical path for stain \"CD20\" for slide \"HTA9_1_19383\" of study \"2.25.56219147941526607962658668060030231728\" \n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19372\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19398\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19348\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19387\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19392\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19370\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19407\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19374\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19385\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19357\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19384\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19386\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19353\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19365\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19355\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19377\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19367\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19394\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19349\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19393\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19362\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19347\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19401\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19382\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19359\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19406\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19351\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19356\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19368\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19397\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19389\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19376\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19395\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19400\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19402\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19381\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19404\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19371\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19354\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19373\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19361\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19391\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.56219147941526607962658668060030231728\" and container \"HTA9_1_19352\"\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.174442227011591161839224535127252003551\" and container \"HTA7_965_1000\"\n",
      "ERROR - skip slides of study \"2.25.174442227011591161839224535127252003551\" and container \"HTA7_965_1000\": Pyramids for different channels and focal planes must have the same structure, i.e., the same number of levels as well as the same dimensions and downsampling factors per level.\n",
      "found n=0 slides\n",
      "search for slides of study \"2.25.207870400800238058337377267796843844207\" and container \"HTA12_10_1108\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_10_1108 d270b226167aadf98a816ac2ccfcefdf390b416bb832b08797ee2969c7ba189e>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.207870400800238058337377267796843844207\" and container \"HTA12_10_1105\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_10_1105 fca80e1c8ef709ca9ccba090e4df1b2e6e0f9cb65a60e6bf0e899b9b2bf70212>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.207870400800238058337377267796843844207\" and container \"HTA12_10_1109\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_10_1109 ad18e486f52c3acdbe625f2f9ef1e3e6a0fa5aee4c6e07b61df1e4bb4b0867ab>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.207870400800238058337377267796843844207\" and container \"HTA12_10_1103\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_10_1103 01b3fa66511a06a358a09086d38ac26fe4a15ce3722ef36a150ab0261f37493a>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.207870400800238058337377267796843844207\" and container \"HTA12_10_1106\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_10_1106 327444aad3e7055e7397f3259eb78af17ce7fe7af7464b8c7e92c335f22a884d>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.207870400800238058337377267796843844207\" and container \"HTA12_10_1102\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA12_10_1102 686f42cc19484e861e11b0abc4fda27b1434709131542e028d785467d274f5e3>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "search for slides of study \"2.25.254901417575324832540235892437527774975\" and container \"HTA7_940_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_940_1000 3b388037ed1042f38c460cbea875db657f1fc35652f2b7f96500ea801b699739>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_940_1000\" of study \"2.25.254901417575324832540235892437527774975\" \n",
      "search for slides of study \"2.25.225599974078887472942035661647638662953\" and container \"HTA7_947_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_947_1000 901752618701ac8da078f660ca724125a28961c4c348777b9f536921624fbb86>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_947_1000\" of study \"2.25.225599974078887472942035661647638662953\" \n",
      "search for slides of study \"2.25.252944744259825394775026913206036790581\" and container \"HTA7_927_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_927_1000 4c6fa9def77f3d0f62063fa6b406eefe16040307c6919f39df48a92df962bcd3>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_927_1000\" of study \"2.25.252944744259825394775026913206036790581\" \n",
      "search for slides of study \"2.25.6018351362280197054240452097367934352\" and container \"HTA7_922_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_922_1000 44915fadb7de05e71bfe7e39009d7f0bfc980149221975fc42e01c7fcf75ab19>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_922_1000\" of study \"2.25.6018351362280197054240452097367934352\" \n",
      "search for slides of study \"2.25.219049900737444567890964056686598614067\" and container \"HTA7_920_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_920_1000 b03b791de567aaded8b96a79fdb6317abd1898495fad138e5cbef3d5009cbf47>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_920_1000\" of study \"2.25.219049900737444567890964056686598614067\" \n",
      "search for slides of study \"2.25.183140175210739429826415953400233623278\" and container \"HTA7_972_1000\"\n",
      "found n=1 slides\n",
      "create presentation states for slide <Slide HTA7_972_1000 5aa2b3d4e8511100355cdde9c70f02f5b7af9320dd0e02767b4c611e9a50470d>\n",
      "create presentation state \"PD1-PDL1-CD45-Ecadherin\"\n",
      "create presentation state \"PanCK-Vimentin-CD45-Ki67\"\n",
      "create presentation state \"CD3-CD20-CD68\"\n",
      "ERROR - could not find an optical path for stain \"CD3\" for slide \"HTA7_972_1000\" of study \"2.25.183140175210739429826415953400233623278\" \n"
     ]
    }
   ],
   "source": [
    "presentation_states = []\n",
    "for (study_instance_uid, container_id), values in slide_info.items():\n",
    "    print(f'search for slides of study \"{study_instance_uid}\" and container \"{container_id}\"')\n",
    "    try:\n",
    "        matched_slides = ds.find_slides(client, study_instance_uid=study_instance_uid, container_id=container_id, pyramid_tolerance=1.0)\n",
    "    except Exception as error:\n",
    "        print(f'ERROR - skip slides of study \"{study_instance_uid}\" and container \"{container_id}\": {error}')\n",
    "    print(f'found n={len(matched_slides)} slides')\n",
    "    for slide in matched_slides:\n",
    "        print(f'create presentation states for slide {slide}')\n",
    "        series_instance_uid = hd.UID()\n",
    "        series_number = 100\n",
    "        instance_number = 1\n",
    "        for group in CHANNEL_GROUPS:\n",
    "            group_name = group['name']\n",
    "            group_settings = group['settings']\n",
    "            print(f'create presentation state \"{group_name}\"')\n",
    "            channels = []\n",
    "            for stain, color in group_settings:\n",
    "                optical_path_identifiers = [\n",
    "                    item[2]\n",
    "                    for item in slide_info[(study_instance_uid, container_id)]\n",
    "                    if item[3] is not None and item[3] == stain\n",
    "                ]\n",
    "                if len(optical_path_identifiers) == 0:\n",
    "                    print(\n",
    "                        f'ERROR - could not find an optical path for stain \"{stain.meaning}\" '\n",
    "                        f'for slide \"{container_id}\" of study \"{study_instance_uid}\" '\n",
    "                    )\n",
    "                    continue\n",
    "                channel_index = slide.get_channel_index(\n",
    "                    channel_identifier=optical_path_identifiers[0],\n",
    "                    channel_type='OPTICAL_PATH'\n",
    "                )\n",
    "                volume_images = slide.get_volume_images(\n",
    "                    channel_index=channel_index\n",
    "                )\n",
    "                thumbnail_image = volume_images[-1]\n",
    "                matrix = thumbnail_image.get_total_pixel_matrix(channel_index=0)\n",
    "                pixel_array = np.squeeze(matrix[:, :, 0])\n",
    "                voi_range = compute_limit_values(pixel_array)\n",
    "                ch = Channel(\n",
    "                    [image.metadata for image in volume_images],\n",
    "                    (voi_range[0], voi_range[1] * 2.0),\n",
    "                    color.value\n",
    "                )\n",
    "                channels.append(ch)\n",
    "                \n",
    "            if len(channels) < 2:\n",
    "                print(\n",
    "                    'WARNING - skip presentation state for '\n",
    "                    f'slide \"{container_id}\" of study \"{study_instance_uid}\" '\n",
    "                    'because of lack of matching optical paths'\n",
    "                )\n",
    "                continue\n",
    "                \n",
    "            pr_instance = create_presentation_state(\n",
    "                channels,\n",
    "                series_instance_uid,\n",
    "                series_number,\n",
    "                instance_number\n",
    "            )\n",
    "            instance_number += 1\n",
    "            presentation_states.append(pr_instance)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5b8be0cd-1be5-49a0-bebd-37d498903f3a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# client.store_instances(presentation_states)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "id": "de193b66-a392-4cd8-9d41-8baec9dd5c34",
   "metadata": {},
   "outputs": [],
   "source": [
    "data_dir = Path('data')\n",
    "data_inventory_rows = []\n",
    "for state in presentation_states:\n",
    "    container_id = state.ContainerIdentifier\n",
    "    content_description = state.ContentDescription.replace(' ', '').replace('(2)', '')\n",
    "    filename = f'{study_instance_uid}_{container_id}_{content_description}.dcm'\n",
    "    filepath = data_dir.joinpath(filename)\n",
    "    state.save_as(filepath)\n",
    "    data_inventory_rows.append({\n",
    "        'Filename': filename,\n",
    "        'SOP Instance UID': state.SOPInstanceUID,\n",
    "        'Patient ID': state.PatientID,\n",
    "        'Clinical Trial Protocol ID': state.ClinicalTrialProtocolID,\n",
    "        'Study Instance UID': state.StudyInstanceUID,\n",
    "        'Series Instance UID': state.SeriesInstanceUID\n",
    "    })\n",
    "data_inventory_filepath = data_dir.joinpath('inventory.txt')\n",
    "data_inventory = pd.DataFrame(data_inventory_rows)\n",
    "data_inventory.to_csv(data_inventory_filepath, sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "id": "98036c15-82e5-4953-af33-7e6c1f633f0b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "105"
      ]
     },
     "execution_count": 57,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(set([state.ReferencedSeriesSequence[0].SeriesInstanceUID for state in presentation_states]))"
   ]
  }
 ],
 "metadata": {
  "environment": {
   "kernel": "python3",
   "name": "common-cpu.m93",
   "type": "gcloud",
   "uri": "gcr.io/deeplearning-platform-release/base-cpu:m93"
  },
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}