-
Notifications
You must be signed in to change notification settings - Fork 7
/
napari-amdtrk.json
137 lines (137 loc) · 9.27 KB
/
napari-amdtrk.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
{
"name": "napari-amdtrk",
"display_name": "Amend segmentation and track",
"visibility": "public",
"icon": "",
"categories": [],
"schema_version": "0.2.1",
"on_activate": null,
"on_deactivate": null,
"contributions": {
"commands": [
{
"id": "napari-amdtrk.get_reader",
"title": "Open data with Amend segmentation and track",
"python_name": "napari_amdtrk._reader:napari_get_reader",
"short_title": null,
"category": null,
"icon": null,
"enablement": null
},
{
"id": "napari-amdtrk.make_sample_data",
"title": "Load sample data from Amend segmentation and track",
"python_name": "napari_amdtrk._sample_data:make_sample_data",
"short_title": null,
"category": null,
"icon": null,
"enablement": null
},
{
"id": "napari-amdtrk.make_amdtrkwidget",
"title": "Make amend track widget",
"python_name": "napari_amdtrk._widget:AmdTrkWidget",
"short_title": null,
"category": null,
"icon": null,
"enablement": null
}
],
"readers": [
{
"command": "napari-amdtrk.get_reader",
"filename_patterns": [
"*"
],
"accepts_directories": true
}
],
"writers": null,
"widgets": [
{
"command": "napari-amdtrk.make_amdtrkwidget",
"display_name": "Amend track widget",
"autogenerate": true
}
],
"sample_data": [
{
"key": "napari-amdtrk - simple",
"display_name": "basic tracks",
"uri": "simple",
"reader_plugin": null
},
{
"key": "napari-amdtrk - full",
"display_name": "complete cell cycle tracks",
"uri": "full",
"reader_plugin": null
}
],
"themes": null,
"menus": {},
"submenus": null,
"keybindings": null,
"configuration": []
},
"package_metadata": {
"metadata_version": "2.1",
"name": "napari-amdtrk",
"version": "1.1.0",
"dynamic": null,
"platform": null,
"supported_platform": null,
"summary": "Manually amend segmentation and track within napari",
"description": "# napari-amdtrk\n\n[](https://github.com/Jeff-Gui/napari-amdtrk/raw/main/LICENSE)\n[](https://pypi.org/project/napari-amdtrk)\n[](https://python.org)\n[](https://github.com/Jeff-Gui/napari-amdtrk/actions)\n[](https://codecov.io/gh/Jeff-Gui/napari-amdtrk)\n[](https://napari-hub.org/plugins/napari-amdtrk)\n\nAmend segmentation and track within napari manually.\n\n<img src=\"preview.png\" alt=\"overview\" width=\"900\" />\n\n\n### [:eyes: watch a demo video](https://drive.google.com/file/d/1oHPdYcKv-QgOWylm21DnOF1NlVNsRIcL/view)\n\n----------------------------------\n\n### Input data structure\n\nNapari-amdtrk reads an input directory which includes:\n- An intensity image (`tif`) in txyc (or txy) format\n- An object mask (`tif`) in txy format\n- An object table (`csv`) with following essential columns:\n - frame: time frame\n - trackId: ID of the track, starting from 1\n - Center_of_the_object_0: x coordinate\n - Center_of_the_object_1: y coordinate\n - continuous_label: the corresponding label (intensity value) of the object in the object mask (You may use `skimage.measure.label` to get it from a binary mask).\n\n- A config file named `config.yaml` (_other names are not allowed_)\n\n Within the config file, there should be:\n - intensity_suffix: suffix of the intensity image (e.g., for `foo_GFP.tif`, use `GFP` in the config). For multiple intensity images, separate them with commas (e.g., `GFP, mCherry`)\n - mask_suffix: suffix of the mask image\n - track_suffix: suffix of the tracked object table\n - frame_base: index of the first frame (either `0` or `1`)\n - stateCol: __optional__ column name for the cell state (e.g., cell cycle phase) in the object table. Leave blank if the object table does not contain it\n\n__Napari-amdtrk will modify mask and track files in place.__ Other files are not affected.\n\n---\n### Quick start\n\n1. Open `napari` GUI.\n2. `File` > `Open folder` > choose `Amend segmentation and track`\n3. `Plugins` > `napari-amdtrk: Amend track widget` > `Run`\n4. In `layer list`, select the `segm` layer to start editing.\n\nPlease check out the demo video [here](https://drive.google.com/file/d/1oHPdYcKv-QgOWylm21DnOF1NlVNsRIcL/view) and the sample data (see below).\n\n----------------------------------\n\n### Sample data\n\nTo load sample data, `File` > `Open Sample` > `napari-amdtrk` > `basic tracks` or `complete cell cycle tracks`.\n\n- basic tracks: simple cell tracks as essential input data.\n- complete cell cycle tracks: cell tracks with additional cell cycle features.\n\nThe above operations will download data to `~/.amd_trk/_sample_data/` (__~230MB__). After downloading is finished, sample data will be loaded.\n\n_Notes_\n- Please cite this repository if using the plugin in your work (try `About` > `Cite this repository` upper right of this homepage).\n \n- Sample data (cell track videos) have been published with [_pcnaDeep: a fast and robust single-cell tracking method using deep-learning mediated cell cycle profiling_](10.1093/bioinformatics/btac602). We acknowledge Dr Kuan Yoow Chan and members of his lab for generating the data. \n\n----------------------------------\n\n### Keyboard shortcuts\n\n- <kbd>↑</kbd> and <kbd>↓</kbd>: toggle different operations\n- <kbd>enter</kbd>: run the operation\n\n- Available to a selected object:\n - <kbd>control</kbd> + <kbd>9</kbd>: shrink the object mask\n - <kbd>control</kbd> + <kbd>0</kbd>: expand the object mask\n\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Installation\n\nPlease install `napari` GUI first:\n\n python -m pip install \"napari[all]\"\n\nYou can install `napari-amdtrk` via [pip]:\n\n pip install napari-amdtrk\n\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-amdtrk\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n",
"description_content_type": "text/markdown",
"keywords": null,
"home_page": "https://github.com/Jeff-Gui/napari-amdtrk-plugin",
"download_url": null,
"author": "Yifan Gui",
"author_email": "[email protected]",
"maintainer": null,
"maintainer_email": null,
"license": "MIT",
"classifier": [
"Development Status :: 3 - Alpha",
"Framework :: napari",
"Intended Audience :: Developers",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering :: Image Processing"
],
"requires_dist": [
"numpy (<1.24)",
"magicgui",
"qtpy",
"trackpy",
"pandas",
"scikit-image",
"tox ; extra == 'testing'",
"pytest ; extra == 'testing'",
"pytest-cov ; extra == 'testing'",
"pytest-qt ; extra == 'testing'",
"napari ; extra == 'testing'",
"pyqt5 ; extra == 'testing'"
],
"requires_python": ">=3.8",
"requires_external": null,
"project_url": [
"Bug Tracker, https://github.com/Jeff-Gui/napari-amdtrk-plugin/issues",
"Documentation, https://github.com/Jeff-Gui/napari-amdtrk-plugin/blob/master/README.md",
"Source Code, https://github.com/Jeff-Gui/napari-amdtrk-plugin"
],
"provides_extra": [
"testing"
],
"provides_dist": null,
"obsoletes_dist": null
},
"npe1_shim": false
}