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manifest.imjoy.json
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manifest.imjoy.json
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{
"name": "ImJoy Repository",
"description": "ImJoy plugin repository.",
"uri_root": "",
"version": "0.2.0",
"plugins": [
{
"name": "CreateNumberedLabels",
"type": "native-python",
"version": "0.0.1",
"description": "Created numbered label images.",
"tags": [
"stable",
"dev"
],
"ui": [
"<span style='font-weight: 550; color:#666362'>Path LABELS</span>: {id: 'path_labels', type: 'string', placeholder: 'paste-path-to-labels'}",
"<span style='font-weight: 550; color:#666362'>File string</span>: {id: 'file_ident', type: 'string', placeholder: 'mask__'}",
"<span style='font-weight: 550; color:#666362'>Img extension</span>: {id: 'img_ext', type: 'string', placeholder: '.png'}"
],
"cover": "",
"inputs": null,
"outputs": null,
"flags": [],
"icon": "extension",
"api_version": "0.1.7",
"env": "",
"permissions": [],
"requirements": {
"dev": [
""
],
"stable": [
"pip: -U git+https://github.com/fish-quant/fq-segmentation@master"
]
},
"dependencies": [],
"uri": "imjoy-plugins\\CreateNumberedLabels.imjoy.html"
},
{
"name": "ObjectDist",
"type": "native-python",
"version": "0.2.1",
"description": "Pre-process 3D images to obtain 2D images for segmentation.",
"tags": [
"stable",
"dev"
],
"ui": [
"Path DATA: {id: 'path_scan', type: 'string', placeholder: 'paste-path-to-data'}",
"Path SAVE: {id: 'path_save', type: 'string', placeholder: 'segmentation-results˃˃distance-maps'}",
"String channel: {id: 'str_label', type: 'string', placeholder: 'mask__nuclei__'}",
"String save INDEX: {id: 'str_save_ind', type: 'string', placeholder: 'nuclei_close_ind__'}",
"String save DIST: {id: 'str_save_dist', type: 'string', placeholder: 'nuclei_close_dist__'}",
"Truncate distance: {id: 'truncate_distance', type: 'number', placeholder: 255}",
"Search recursive: {id: 'search_recursive', type: 'choose', options: ['false', 'true'], placeholder: 'false'}"
],
"cover": "",
"inputs": null,
"outputs": null,
"flags": [],
"icon": "extension",
"api_version": "0.1.7",
"env": "",
"permissions": [],
"requirements": {
"dev": [
""
],
"stable": [
"pip: -U git+https://github.com/fish-quant/fq-segmentation@master scikit-image"
]
},
"dependencies": [],
"uri": "imjoy-plugins\\ObjectDist.imjoy.html"
},
{
"name": "PreProcess",
"type": "native-python",
"version": "0.2.0",
"description": "Pre-process 3D images to obtain 2D images for segmentation.",
"tags": [
"stable",
"dev"
],
"ui": [
"<span style='font-weight: 550; color:#666362'>Path DATA</span>: {id: 'path_process', type: 'string', placeholder: 'paste-path-to-data'}",
"<span style='font-weight: 550; color:#666362'>Path SAVE</span>: {id: 'path_save', type: 'string', placeholder: 'acquisition˃˃analysis'}",
"<span style='font-weight: 550; color:#666362'>Subfolder</span>: {id: 'subfolder', type: 'string', placeholder: 'segmentation-input'}",
"<span style='font-weight: 550; color:#666362'>Channel string</span>: {id: 'channel_ident', type: 'string', placeholder: 'dapi'}",
"<span style='font-weight: 550; color:#666362'>Img extension</span>: {id: 'img_ext', type: 'string', placeholder: '.tif'}",
"<span style='font-weight: 550; color:#666362'>Projection type</span>: {id: 'projection_type', type: 'choose', options: ['max', 'mean','indiv'], placeholder: 'max'}",
"<span style='font-weight: 550; color:#666362'>Search recursive</span>: {id: 'search_recursive', type: 'choose', options: ['false', 'true'], placeholder: 'false'}"
],
"cover": "",
"inputs": null,
"outputs": null,
"flags": [],
"icon": "extension",
"api_version": "0.1.7",
"env": "",
"permissions": [],
"requirements": {
"dev": [
""
],
"stable": [
"pip: -U git+https://github.com/fish-quant/fq-segmentation@master"
]
},
"dependencies": [],
"uri": "imjoy-plugins\\PreProcess.imjoy.html"
},
{
"name": "SegmentCellsNuclei",
"type": "native-python",
"version": "0.2.2",
"description": "Segment cells AND nuclei.",
"tags": [
"stable",
"dev"
],
"ui": [
"<span style='font-weight: 550; color:#666362'>Path DATA</span>: {id: 'path_scan', type: 'string', placeholder: 'paste-path-to-data'}",
"<span style='font-weight: 550; color:#666362'>Input subfolder</span>: {id: 'input_subfolder', type: 'string', placeholder: 'segmentation-input'}",
"<span style='font-weight: 550; color:#666362'>Path SAVE</span>: {id: 'path_save', type: 'string', placeholder: 'segmentation-input˃˃segmentation-results'}",
"<span style='font-weight: 550; color:#666362'>String CELLS</span>: {id: 'str_cyto', type: 'string', placeholder: 'cy3'}",
"<span style='font-weight: 550; color:#666362'>String NUCLEI</span>: {id: 'str_nuclei', type: 'string', placeholder: 'dapi'}",
"<span style='font-weight: 550; color:#666362'>Scaling factor/New size: </span>: {id: 'new_size', type: 'string', placeholder: '2'}",
"<span style='font-weight: 550; color:#666362'>Size CELLS</span>: {id: 'size_cells', type: 'number', placeholder: 200}",
"<span style='font-weight: 550; color:#666362'>Size NUCLEI</span>: {id: 'size_nuclei', type: 'number', placeholder: 100}",
"<span style='font-weight: 550; color:#666362'>Net Average</span>: {id: 'net_avg', type: 'choose', options: ['false', 'true'], placeholder: 'false'}",
"<span style='font-weight: 550; color:#666362'>Resample</span>: {id: 'resample', type: 'choose', options: ['false', 'true'], placeholder: 'false'}",
"<span style='font-weight: 550; color:#666362'>String img ext</span>: {id: 'img_ext', type: 'string', placeholder: '.png'}"
],
"cover": "https://fq-segmentation.readthedocs.io/en/latest/img/segmentation__cells.png",
"inputs": null,
"outputs": null,
"flags": [],
"icon": "extension",
"api_version": "0.1.7",
"env": "",
"permissions": [],
"requirements": {
"dev": [
""
],
"stable": [
"pip: -U git+https://github.com/fish-quant/fq-segmentation@master"
]
},
"dependencies": [],
"uri": "imjoy-plugins\\SegmentCellsNuclei.imjoy.html"
},
{
"name": "SegmentObjects",
"type": "native-python",
"version": "0.2.2",
"description": "Segment cells OR nuclei.",
"tags": [
"stable",
"dev"
],
"ui": [
"<span style='font-weight: 550; color:#666362'>Path DATA</span>: {id: 'path_scan', type: 'string', placeholder: 'paste-path-to-data'}",
"<span style='font-weight: 550; color:#666362'>Input subfolder</span>: {id: 'input_subfolder', type: 'string', placeholder: 'segmentation-input'}",
"<span style='font-weight: 550; color:#666362'>Path SAVE</span>: {id: 'path_save', type: 'string', placeholder: 'segmentation-input˃˃segmentation-results'}",
"<span style='font-weight: 550; color:#666362'>String channel</span>: {id: 'str_channel', type: 'string', placeholder: 'dapi'}",
"<span style='font-weight: 550; color:#666362'>Object name</span>: {id: 'obj_name', type: 'string', placeholder: 'nuclei'}",
"<span style='font-weight: 550; color:#666362'>Cellpose model</span>: {id: 'model_type', type: 'choose', options: ['nuclei', 'cyto'], placeholder: 'nuclei'}",
"<span style='font-weight: 550; color:#666362'>Scaling factor/New size:</span>: {id: 'new_size', type: 'string', placeholder: '1'}",
"<span style='font-weight: 550; color:#666362'>Object diameter</span>: {id: 'diameter', type: 'number', placeholder: 100}",
"<span style='font-weight: 550; color:#666362'>Net Average</span>: {id: 'net_avg', type: 'choose', options: ['false', 'true'], placeholder: 'false'}",
"<span style='font-weight: 550; color:#666362'>Resample</span>: {id: 'resample', type: 'choose', options: ['false', 'true'], placeholder: 'false'}",
"<span style='font-weight: 550; color:#666362'>String img ext</span>: {id: 'img_ext', type: 'string', placeholder: '.png'}"
],
"cover": "https://fq-segmentation.readthedocs.io/en/latest/img/segmentation__cells.png",
"inputs": null,
"outputs": null,
"flags": [],
"icon": "extension",
"api_version": "0.1.7",
"env": "",
"permissions": [],
"requirements": {
"dev": [
""
],
"stable": [
"pip: -U git+https://github.com/fish-quant/fq-segmentation@master"
]
},
"dependencies": [],
"uri": "imjoy-plugins\\SegmentObjects.imjoy.html"
}
],
"collections": []
}