diff --git a/aiod_registry/manifests/cellpose.json b/aiod_registry/manifests/cellpose.json new file mode 100644 index 0000000..3c99cee --- /dev/null +++ b/aiod_registry/manifests/cellpose.json @@ -0,0 +1,180 @@ +{ + "name": "Cellpose", + "short_name": "cellpose", + "metadata": { + "description": "Cellpose is a generalist model for cell and nucleus segmentation.", + "url": "https://cellpose.readthedocs.io/en/latest/", + "repo": "https://github.com/MouseLand/cellpose", + "pubs": [ + { + "info": "Cellpose v1", + "url": "https://doi.org/10.1038/s41592-020-01018-x", + "title": "Cellpose: a generalist algorithm for cellular segmentation", + "doi": "10.1038/s41592-020-01018-x", + "authors": [ + { + "name": "Carsen Stringer", + "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA" + }, + { + "name": "Tim Wang", + "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA" + }, + { + "name": "Michalis Michaelos", + "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA" + }, + { + "name": "Marius Pachitariu", + "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA" + } + ] + }, + { + "info": "Cellpose v2", + "url": "https://doi.org/10.1038/s41592-022-01663-4", + "title": "Cellpose 2.0: how to train your own model", + "doi": "10.1038/s41592-022-01663-4", + "authors": [ + { + "name": "Marius Pachitariu", + "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA" + }, + { + "name": "Carsen Stringer", + "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA" + } + ] + }, + { + "info": "Cellpose v3", + "url": "https://www.biorxiv.org/content/10.1101/2024.02.10.579780v2", + "title": "Cellpose3: one-click image restoration for improved cellular segmentation", + "doi": "10.1101/2024.02.10.579780", + "authors": [ + { + "name": "Carsen Stringer", + "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA" + }, + { + "name": "Marius Pachitariu", + "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA" + } + ] + } + ] + }, + "versions": { + "cyto3": { + "tasks": { + "cyto": { + "location":"https://www.cellpose.org/models/cyto3" + } + } + }, + "nuclei": { + "tasks": { + "nuclei": { + "location": "https://www.cellpose.org/models/nucleitorch_0" + } + } + }, + "cyto1": { + "tasks": { + "cyto": { + "location": "https://www.cellpose.org/models/cytotorch_0" + } + } + }, + "cyto2": { + "tasks": { + "cyto": { + "location":"https://www.cellpose.org/models/cyto2torch_0" + } + } + } + }, + "params": [ + { + "name": "Diameter", + "arg_name": "diameter", + "value": 0, + "tooltip": "Diameter of the cells in pixels. If None or 0, Cellpose will try to estimate it. Setting the value may improve results. See https://cellpose.readthedocs.io/en/latest/settings.html#diameter for details." + }, + { + "name": "Segment Channel", + "arg_name": "segment_channel", + "value": 0, + "tooltip": "What channel to segment on. 0=grayscale, 1=red, 2=green, 3=blue. See https://cellpose.readthedocs.io/en/latest/settings.html#channels for details." + }, + { + "name": "Nucleus Channel", + "arg_name": "nucleus_channel", + "value": 0, + "tooltip": "What channel contains nucleus. 0=grayscale, 1=red, 2=green, 3=blue. Unused for 'nuclei' model, where nuclei are in the segment channel. See https://cellpose.readthedocs.io/en/latest/settings.html#channels for details." + }, + { + "name": "3D Segmentation", + "arg_name": "do_3D", + "value": false, + "tooltip": "Whether to do 3D segmentation. If True, will try to segment in 3D (XY, XZ, YZ). If False, will segment in 2D and combine with stitch_threshold." + }, + { + "name": "Stitch Threshold", + "arg_name": "stitch_threshold", + "value": 0.0, + "tooltip": "Threshold for stitching 2D segmentations together. Value is the IoU that constitutes an overlap and thus merge. Only used if do_3D is False and >0." + }, + { + "name": "Cellprob Threshold", + "arg_name": "cellprob_threshold", + "value": 0.0, + "tooltip": "Threshold for flows to determine ROIs. Decrease to find more & larger ROIs, increase if too many ROIs (esp. in dim regions). See https://cellpose.readthedocs.io/en/latest/settings.html#cellprob-threshold for details." + }, + { + "name": "Flow Threshold", + "arg_name": "flow_threshold", + "value": 0.4, + "tooltip": "Threshold for flows to determine ROIs. Not used for 3D. See https://cellpose.readthedocs.io/en/latest/settings.html#cellprob-threshold for details." + }, + { + "name": "Num Iterations", + "arg_name": "niter", + "value": 0, + "tooltip": "Number of iterations to simulate dynamics for. By default (0/None), proportional to ROI diameter. See https://cellpose.readthedocs.io/en/latest/settings.html#number-of-iterations-niter for details." + }, + { + "name": "Anisotropy", + "arg_name": "anisotropy", + "value": null, + "dtype": "float", + "tooltip": "Optional rescaling factor for Z (e.g. set to 2.0 if Z is sampled half as dense as X or Y)." + }, + { + "name": "Channel axis", + "arg_name": "channel_axis", + "value": null, + "dtype": "int", + "tooltip": "Set the axis where channels are stored. 'None' means it tries to figure it out - useful if no/poor metadata and not loading properly." + }, + { + "name": "Z axis", + "arg_name": "z_axis", + "value": null, + "dtype": "int", + "tooltip": "Set the axis where Z slices are stored. 'None' means it tries to figure it out - useful if no/poor metadata and not loading properly." + }, + { + "name": "Batch size", + "arg_name": "batch_size", + "value": 64, + "tooltip": "Number of 224x224 patches to run simultaneously on the GPU. Can make smaller or bigger depending on GPU memory usage." + }, + { + "name": "Minimum size", + "arg_name": "min_size", + "value": 15, + "tooltip": "Size (in pixels) of ROIs/to remove if lower. 0 will not remove any masks." + } + ] +} \ No newline at end of file