v0.2.3 Release (#127)

Version 0.2.3 Co-authored-by: Patrick Cleeve <[email protected]> Co-authored-by: LucileNaegele <[email protected]>
DeMarcoLab · Sep 8, 2023 · c2d76a9 · c2d76a9
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diff --git a/.gitignore b/.gitignore
@@ -24,3 +24,4 @@ waffle/*
 old_protocol/*.y*ml
 old_protocol/*
 dist/*
+autolamella/db/fibsem.db
diff --git a/README.md b/README.md
@@ -1,4 +1,6 @@
-## Overview
+[![image](http://img.shields.io/pypi/v/autolamella.svg)](https://pypi.python.org/pypi/autolamella/)
+
+# Overview
 
 AutoLamella is a python package for automated cryo-lamella preparation with focused ion beam milling. It is based on [openFIBSEM](https://github.com/DeMarcoLab/fibsem), and currently supports the [TESCAN Automation SDK](https://www.tescan.com/en/products/automation-sdk/) and [ThermoFisher AutoScript](https://www.tescan.com/en/products/autoscript/). Support for other FIBSEM systems is planned.
 

diff --git a/autolamella/config.py b/autolamella/config.py
@@ -68,3 +68,7 @@
     "distance": 10.e-6,
 }
 }
+
+
+####### FEATURE FLAGS
+_MINIMAP_VISUALISATION = True
diff --git a/autolamella/default_protocol.yaml → ...lamella/depreceated/default_protocol.yaml b/autolamella/default_protocol.yaml → ...lamella/depreceated/default_protocol.yaml
diff --git a/autolamella/protocol_bacteria.yaml → ...amella/depreceated/protocol_bacteria.yaml b/autolamella/protocol_bacteria.yaml → ...amella/depreceated/protocol_bacteria.yaml
diff --git a/autolamella/protocol_converter.py → ...lamella/depreceated/protocol_converter.py b/autolamella/protocol_converter.py → ...lamella/depreceated/protocol_converter.py
diff --git a/autolamella/protocol_ruby.yaml → autolamella/depreceated/protocol_ruby.yaml b/autolamella/protocol_ruby.yaml → autolamella/depreceated/protocol_ruby.yaml
diff --git a/autolamella/napari.yaml b/autolamella/napari.yaml
@@ -5,7 +5,7 @@ contributions:
 
       # Widgets
     - id: autolamella.viewer
-      python_name: autolamella.autolamella_ui:UiInterface
+      python_name: autolamella.ui.AutoLamellaUI:AutoLamellaUI
       title: AutoLamella UI
 
   widgets:

diff --git a/autolamella/notebook.ipynb b/autolamella/notebook.ipynb
@@ -236,7 +236,7 @@
     "positions = {\n",
     "    \"MillTrench\": [],\n",
     "    \"MillUndercut\": [],\n",
-    "    \"SetupLamella\": [],\n",
+    "    \"ReadyLamella\": [],\n",
     "}\n",
     "for lamella in exp.positions:\n",
     "    for state in lamella.history:\n",
@@ -276,7 +276,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = _tile._plot_positions(eb_image, positions[\"SetupLamella\"], show=True)\n",
+    "fig = _tile._plot_positions(eb_image, positions[\"ReadyLamella\"], show=True)\n",
     "fig.savefig(os.path.join(PATH, \"overview-positions-mill-lamella.png\"), dpi=300, bbox_inches='tight')"
    ]
   },
@@ -414,6 +414,13 @@
     "plt.show()\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/autolamella/protocol/protocol-base.yaml b/autolamella/protocol/protocol-base.yaml
@@ -0,0 +1,140 @@
+
+name: autolamella-base-scan-rotation-0deg
+method: default # waffle or default
+
+options:
+  supervise:
+    trench: false
+    undercut: true
+    setup_lamella: true
+    features: true
+    lamella: true
+    mill_rough: true
+    mill_regular: true
+    mill_polishing: true
+
+fiducial:
+  enabled: true
+  height: 10.e-6
+  width: 1.e-6
+  depth: 1.0e-6
+  rotation: 45
+  milling_current: 2.0e-9
+  preset: "30 keV; 20 nA" # TESCAN only
+  application_file: autolamella
+  cleaning_cross_section: false
+  passes: null
+  hfw: 80.e-6
+
+
+trench:
+  lamella_width: 22.e-6
+  lamella_height: 30.0e-6
+  milling_current: 28.0e-9
+  trench_height: 32.e-6
+  depth: 2.5e-6
+  offset: 0.0e-6
+  size_ratio: 2.0
+  preset: "30 keV; 2.5 nA" # TESCAN only
+  hfw: 180.0e-6
+  application_file: autolamella
+  cleaning_cross_section: false
+
+lamella:
+  beam_shift_attempts: 3.0
+  alignment_current: "Imaging"
+  lamella_width: 20.e-6
+  lamella_height: 800.e-9
+  stages:
+    -   application_file: autolamella
+        cleaning_cross_section: false
+        depth: 6.5e-07
+        dwell_time: 1.0e-06
+        hfw: 7.999999999999999e-05
+        lamella_height: 8.0e-07
+        lamella_width: 6.0e-06
+        milling_current: 7.4e-10
+        offset: 2.0e-06
+        patterning_mode: Serial
+        preset: ''
+        rate: 0.0001
+        size_ratio: 1.0
+        spot_size: 5.0e-08
+        trench_height: 3.5e-06
+    -   application_file: autolamella
+        cleaning_cross_section: true
+        depth: 6.5e-07
+        dwell_time: 1.0e-06
+        hfw: 7.999999999999999e-05
+        lamella_height: 8.0e-07
+        lamella_width: 6.0e-06
+        milling_current: 2.0e-10
+        offset: 5.0e-07
+        patterning_mode: Serial
+        preset: ''
+        rate: 0.0001
+        size_ratio: 1.0
+        spot_size: 5.0e-08
+        trench_height: 2.0e-06
+    -   application_file: autolamella
+        cleaning_cross_section: true
+        depth: 4.0e-07
+        dwell_time: 1.0e-06
+        hfw: 7.999999999999999e-05
+        lamella_height: 6.0e-07
+        lamella_width: 6.0e-06
+        milling_current: 6.0e-11
+        offset: 0.0
+        patterning_mode: Serial
+        preset: ''
+        rate: 0.0001
+        size_ratio: 1.0
+        spot_size: 5.0e-08
+        trench_height: 5.0e-07
+
+
+microexpansion:
+  width: 0.5e-6
+  height: 18.e-6
+  depth: 1.0e-6
+  distance: 10.e-6 # Does not include Lamella width. So centre of microexpansion is lamella_width/2 + distance.
+  milling_current: 2.e-9
+  preset: "30 keV; 2.5 nA" # TESCAN only
+  hfw: 200e-6
+  application_file: autolamella
+  cleaning_cross_section: false
+  lamella_width: 10.e-6
+
+
+
+notch:
+  enabled: false
+  vheight: 2.0e-6
+  vwidth: 0.2e-6
+  hwidth: 2.0e-6
+  hheight: 0.2e-6
+  depth: 5.0e-6
+  distance: 5.0e-6
+  flip: 0
+  milling_current: 2.e-9
+  preset: "30 keV; 2.5 nA" # TESCAN only
+  hfw: 80e-6
+  application_file: autolamella
+  cleaning_cross_section: false
+
+autolamella_undercut:
+  width: 10.e-6
+  height: 4.e-6
+  depth: 2.0e-6
+  milling_current: 7.6e-9
+  preset: "30 keV; 2.5 nA" # TESCAN only
+  hfw: 80.0e-6
+  application_file: autolamella
+  tilt_angle: -10
+  tilt_angle_step: 2
+  cleaning_cross_section: false
+
+ml:
+    encoder: resnet34
+    num_classes: 3
+    checkpoint: autolamella-05-34.pt
diff --git a/autolamella/protocol/protocol-chromatin.yaml b/autolamella/protocol/protocol-chromatin.yaml
@@ -9,6 +9,9 @@ options:
     setup_lamella: true
     features: true
     lamella: true
+    mill_rough: true
+    mill_regular: true
+    mill_polishing: true
 
 fiducial:
   enabled: true
@@ -93,7 +96,7 @@ lamella:
         depth: 4.0e-07
         dwell_time: 1.0e-06
         hfw: 7.999999999999999e-05
-        lamella_height: 4.0e-07
+        lamella_height: 5.0e-07
         lamella_width: 6.0e-06
         milling_current: 6.0e-11
         offset: 0.0
@@ -149,4 +152,4 @@ autolamella_undercut:
 ml:
     encoder: resnet34
     num_classes: 3
-    weights: model4.pt
+    checkpoint: autolamella-05-34.pt
diff --git a/autolamella/protocol/protocol-waffle.yaml b/autolamella/protocol/protocol-waffle.yaml
@@ -0,0 +1,124 @@
+autolamella_undercut:
+    application_file: autolamella
+    cleaning_cross_section: false
+    depth: 2.5e-06
+    height: 16.0e-06
+    hfw: 8.0e-05
+    milling_current: 7.6e-09
+    preset: 30 keV; 2.5 nA
+    tilt_angle: -5.0
+    tilt_angle_step: 2.0
+    width: 22.0e-6
+    type: Rectangle
+fiducial:
+    application_file: autolamella
+    cleaning_cross_section: false
+    depth: 1.5e-06
+    enabled: true
+    height: 1.0e-05
+    hfw: 8.0e-05
+    milling_current: 7.6e-09
+    passes: null
+    preset: 30 keV; 20 nA
+    rotation: 45
+    width: 1.0e-06
+    type: Fiducial
+lamella:
+    alignment_current: Imaging Current
+    beam_shift_attempts: 3.0
+    lamella_height: 8.0e-07
+    lamella_width: 1.0e-05
+    stages:
+    -   application_file: autolamella
+        cleaning_cross_section: true
+        depth: 2.0e-06
+        hfw: 8.0e-05
+        lamella_height: 6.5e-07
+        lamella_width: 14.0e-6
+        milling_current: 2.0e-09
+        offset: 2.0e-06
+        preset: 30 keV; 2.5 nA
+        size_ratio: 1.0
+        trench_height: 5.0e-06
+        type: Trench
+    -   application_file: autolamella
+        cleaning_cross_section: true
+        depth: 1.0e-06
+        hfw: 8.0e-05
+        lamella_height: 6.5e-07
+        lamella_width: 1.4e-05
+        milling_current: 7.4e-10
+        offset: 5.0e-07
+        preset: 30 keV; 1 nA
+        size_ratio: 1.0
+        trench_height: 2.0e-06
+        type: Trench
+    -   application_file: autolamella
+        cleaning_cross_section: true
+        depth: 4.0e-07
+        hfw: 8.0e-05
+        lamella_height: 6.5e-07
+        lamella_width: 1.4e-05
+        milling_current: 6.0e-11
+        offset: 0.0
+        preset: 30 keV; 50 pA
+        size_ratio: 1.0
+        trench_height: 6.0e-07
+        type: Trench
+method: waffle
+microexpansion:
+    application_file: autolamella
+    cleaning_cross_section: false
+    depth: 1.0e-06
+    distance: 1.0e-05
+    height: 1.8e-05
+    hfw: 200e-6
+    lamella_width: 1.0e-05
+    milling_current: 2.0e-09
+    preset: 30 keV; 2.5 nA
+    width: 5.0e-07
+    type: MicroExpansion
+ml:
+    encoder: resnet34
+    num_classes: 3
+    checkpoint: autolamella-05-34.pt
+name: autolamella-waffle-scan-rotation-0deg
+notch:
+    application_file: autolamella
+    cleaning_cross_section: false
+    depth: 2.5e-06
+    distance: 2.0e-06
+    enabled: true
+    flip: 0
+    hfw: 80e-6
+    hheight: 2.0e-07
+    hwidth: 4.0e-06
+    milling_current: 2.0e-09
+    preset: 30 keV; 2.5 nA
+    vheight: 2.0e-06
+    vwidth: 2.0e-07
+    type: WaffleNotch
+options:
+    compucentric_x_offset: 50.0e-6
+    compucentric_y_offset: 25.0e-6 
+    supervise:
+        features: true
+        setup_lamella: true
+        trench: true
+        undercut: true
+        mill_rough: true
+        mill_regular: true
+        mill_polishing: true
+trench:
+    application_file: autolamella
+    cleaning_cross_section: false
+    depth: 3.0e-06
+    hfw: 0.00018
+    lamella_height: 2.5e-05
+    lamella_width: 2.2e-05
+    milling_current: 7.6e-09
+    offset: 0.0
+    preset: 30 keV; 2.5 nA
+    size_ratio: 2.0
+    trench_height: 3.2e-05
+    type: Trench