aiod-registry 0.1__tar.gz

aiod_registry-0.1/.gitignore

@@ -0,0 +1,62 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Sphinx documentation
+docs/_build/
+
+.DS_Store
+.vscode/
+.idea/
+venv/
+**/_version.py
+/.gitignore

aiod_registry-0.1/.python-version

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+3.12

aiod_registry-0.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Cameron Shand
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

aiod_registry-0.1/PKG-INFO

@@ -0,0 +1,59 @@
+Metadata-Version: 2.4
+Name: aiod-registry
+Version: 0.1
+Summary: A registry of models for use with AI OnDemand (AIoD)
+Project-URL: homepage, https://github.com/FrancisCrickInstitute/aiod_registry
+Project-URL: documentation, https://franciscrickinstitute.github.io/aiod_docs/sections/model_registry/
+Project-URL: source, https://github.com/FrancisCrickInstitute/aiod_registry
+Author-email: Cameron Shand <cameron.shand@crick.ac.uk>, Numan Ahmed <numan.ahmed@crick.ac.uk>, Qin Yu <qin.yu@crick.ac.uk>, Fiona Young <fiona.young@crick.ac.uk>, Jon Smith <jon.smith@crick.ac.uk>
+License-File: LICENSE
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: <3.13,>=3.11
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyyaml
+Provides-Extra: dev
+Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: pytest-cov; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# AIoD Model Registry
+This repository contains the central manifests/schemas that defines the models available within AIoD.
+
+In addition, are:
+
+- Tests for validating schemas
+- Utility functions for ingesting the schemas and filtering by whether a user has access to each model, enabling us to [automatically write the UI for our Napari plugin](https://franciscrickinstitute.github.io/aiod_docs/sections/development/#automatic-ui-construction)
+
+## Installation
+
+```
+git clone https://github.com/FrancisCrickInstitute/AIoD-Model-Registry.git
+cd AIoD-Model-Registry/
+pip install .
+```
+
+or
+
+```
+pip install git+https://github.com/FrancisCrickInstitute/AIoD-Model-Registry.git
+```
+
+## Contact Details
+* cameron.shand@crick.ac.uk
+* jon.smith@crick.ac.uk
+
+## Contribution Guidelines
+See our [documentation](https://franciscrickinstitute.github.io/aiod_docs/sections/contributing/expanding/) for guidance on adding models to this repo.
+
+### Local Validation
+To locally test whether a new manifest is eligible, simply run `pytest -v tests/`, where any errors will be detailed by Pydantic.

aiod_registry-0.1/README.md

@@ -0,0 +1,31 @@
+# AIoD Model Registry
+This repository contains the central manifests/schemas that defines the models available within AIoD.
+
+In addition, are:
+
+- Tests for validating schemas
+- Utility functions for ingesting the schemas and filtering by whether a user has access to each model, enabling us to [automatically write the UI for our Napari plugin](https://franciscrickinstitute.github.io/aiod_docs/sections/development/#automatic-ui-construction)
+
+## Installation
+
+```
+git clone https://github.com/FrancisCrickInstitute/AIoD-Model-Registry.git
+cd AIoD-Model-Registry/
+pip install .
+```
+
+or
+
+```
+pip install git+https://github.com/FrancisCrickInstitute/AIoD-Model-Registry.git
+```
+
+## Contact Details
+* cameron.shand@crick.ac.uk
+* jon.smith@crick.ac.uk
+
+## Contribution Guidelines
+See our [documentation](https://franciscrickinstitute.github.io/aiod_docs/sections/contributing/expanding/) for guidance on adding models to this repo.
+
+### Local Validation
+To locally test whether a new manifest is eligible, simply run `pytest -v tests/`, where any errors will be detailed by Pydantic.

aiod_registry-0.1/aiod_registry/__init__.py

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+from aiod_registry.schema import TASK_NAMES, ModelManifest
+from aiod_registry.utils import get_manifest_paths, load_manifests
+
+__all__ = ["TASK_NAMES", "ModelManifest", "get_manifest_paths", "load_manifests"]

aiod_registry-0.1/aiod_registry/default_configs/cellpose.yaml

@@ -0,0 +1,14 @@
+# Auto-generated by save_all_default_configs - do not edit manually
+diameter: 0
+segment_channel: 0
+nucleus_channel: 0
+do_3D: false
+stitch_threshold: 0.0
+cellprob_threshold: 0.0
+flow_threshold: 0.4
+niter: 0
+anisotropy: null
+channel_axis: null
+z_axis: null
+batch_size: 64
+min_size: 15

aiod_registry-0.1/aiod_registry/default_configs/cellposesam.yaml

@@ -0,0 +1,15 @@
+# Auto-generated by save_all_default_configs - do not edit manually
+segment_channel: 0
+do_3D: false
+resample: true
+stitch_threshold: 0.0
+cellprob_threshold: 0.0
+flow_threshold: 0.4
+niter: 0
+anisotropy: null
+channel_axis: null
+z_axis: null
+batch_size: 64
+min_size: 15
+max_size_fraction: 0.4
+tile_overlap: 0.1

aiod_registry-0.1/aiod_registry/default_configs/empanada.yaml

@@ -0,0 +1,15 @@
+# Auto-generated by save_all_default_configs - do not edit manually
+plane: XY
+downsampling: 1
+conf_threshold: 0.5
+center_threshold: 0.1
+min_distance: 3
+max_objects: 10000
+semantic_only: false
+fine_boundaries: false
+fill_holes_in_segmentation: false
+median_slices: 3
+label_erosion: 0
+label_dilation: 0
+pixel_vote_thr: 2
+allow_one_view: false

aiod_registry-0.1/aiod_registry/default_configs/panseg.yaml

@@ -0,0 +1,20 @@
+# Auto-generated by save_all_default_configs - do not edit manually
+patch: null
+patch_halo: null
+single_batch_mode: true
+model_update: false
+disable_tqdm: false
+ws_threshold: 0.5
+ws_sigma_seeds: 1.0
+ws_stacked: false
+ws_sigma_weights: 2.0
+ws_min_size: 100
+ws_alpha: 1.0
+ws_pixel_pitch: null
+ws_apply_nonmax_suppression: false
+gasp_linkage_criteria: average
+gasp_beta: 0.5
+gasp_post_minsize: 100
+n_threads: 6
+voxel_size: null
+voxel_size_unit: um

aiod_registry-0.1/aiod_registry/default_configs/sam.yaml

@@ -0,0 +1,13 @@
+# Auto-generated by save_all_default_configs - do not edit manually
+points_per_side: 32
+points_per_batch: 64
+pred_iou_thresh: 0.88
+stability_score_thresh: 0.95
+stability_score_offset: 1.0
+box_nms_thresh: 0.7
+crop_n_layers: 0
+crop_nms_thresh: 0.7
+crop_overlap_ratio: 0.34133
+crop_n_points_downscale_factor: 1
+min_mask_region_area: 3
+max_mask_region_area: 0

aiod_registry-0.1/aiod_registry/default_configs/sam2.yaml

@@ -0,0 +1,14 @@
+# Auto-generated by save_all_default_configs - do not edit manually
+points_per_side: 32
+points_per_batch: 64
+pred_iou_thresh: 0.88
+stability_score_thresh: 0.95
+stability_score_offset: 1.0
+box_nms_thresh: 0.7
+crop_n_layers: 0
+crop_nms_thresh: 0.7
+crop_overlap_ratio: 0.34133
+crop_n_points_downscale_factor: 1
+min_mask_region_area: 0
+use_m2m: false
+multimask_output: false

aiod_registry-0.1/aiod_registry/default_configs/stardist.yaml

@@ -0,0 +1,9 @@
+# Auto-generated by save_all_default_configs - do not edit manually
+prob_thresh: null
+nms_thresh: null
+normalize_pmin: 1
+normalize_pmax: 99.8
+n_tiles: null
+normalize_img: true
+scale: null
+channel_idx: 0

aiod_registry-0.1/aiod_registry/manifests/cellpose.json

@@ -0,0 +1,202 @@
+{
+  "name": "Cellpose",
+  "short_name": "cellpose",
+  "metadata": {
+    "description": "Cellpose is a generalist model for cell and nucleus segmentation.",
+    "url": "https://cellpose.readthedocs.io/en/v3.1.1.1/",
+    "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": {
+          "locations": [
+            {
+              "location": "https://www.cellpose.org/models/cyto3"
+            }
+          ]
+        }
+      }
+    },
+    "nuclei": {
+      "tasks": {
+        "nuclei": {
+          "locations": [
+            {
+              "location": "https://www.cellpose.org/models/nucleitorch_0"
+            }
+          ]
+        }
+      }
+    },
+    "cyto1": {
+      "tasks": {
+        "cyto": {
+          "locations": [
+            {
+              "location": "https://www.cellpose.org/models/cytotorch_0"
+            }
+          ]
+        }
+      }
+    },
+    "cyto2": {
+      "tasks": {
+        "cyto": {
+          "locations": [
+            {
+              "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/v3.1.1.1/settings.html#diameter for details."
+    },
+    {
+      "name": "Segment Channel",
+      "arg_name": "segment_channel",
+      "value": 0,
+      "param_type": "channel",
+      "channel_start": 0,
+      "channel_start_label": "Grayscale",
+      "tooltip": "What channel to segment on. Cellpose channel convention: 0=grayscale (no specific channel), 1=first image channel, 2=second image channel, etc. See https://cellpose.readthedocs.io/en/v3.1.1.1/settings.html#channels for details."
+    },
+    {
+      "name": "Nucleus Channel",
+      "arg_name": "nucleus_channel",
+      "value": 0,
+      "param_type": "channel",
+      "channel_start": 0,
+      "channel_start_label": "No nucleus channel",
+      "tooltip": "What channel contains the nucleus. Cellpose channel convention: 0=no nucleus channel (grayscale), 1=first image channel, 2=second image channel, etc. Unused for the 'nuclei' model (nucleus is already the segment channel). See https://cellpose.readthedocs.io/en/v3.1.1.1/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/v3.1.1.1/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/v3.1.1.1/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/v3.1.1.1/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). Only used if do_3D is True."
+    },
+    {
+      "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."
+    }
+  ]
+}

aiod_registry-0.1/aiod_registry/manifests/cellposesam.json

@@ -0,0 +1,143 @@
+{
+  "name": "Cellpose-SAM",
+  "short_name": "cellposesam",
+  "metadata": {
+    "description": "Cellpose-SAM is a generalist model for cell segmentation.",
+    "url": "https://cellpose.readthedocs.io/en/latest/",
+    "repo": "https://github.com/MouseLand/cellpose",
+    "pubs": [
+      {
+        "info": "Cellpose-SAM",
+        "url": "https://doi.org/10.1101/2025.04.28.651001",
+        "title": "Cellpose-SAM: superhuman generalization for cellular segmentation",
+        "doi": "10.1101/2025.04.28.651001",
+        "authors": [
+          {
+            "name": "Marius Pachitariu",
+            "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA"
+          },
+          {
+            "name": "Michael Rariden",
+            "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA"
+          },
+          {
+            "name": "Carsen Stringer",
+            "affiliation": "HHMI Janelia Research Campus, Ashburn, VA, USA"
+          }
+        ]
+      }
+    ]
+  },
+  "versions": {
+    "cpsam": {
+      "tasks": {
+        "cyto": {
+          "locations": [
+            {
+              "location": "https://huggingface.co/mouseland/cellpose-sam/resolve/main/cpsam"
+            }
+          ]
+        },
+        "nuclei": {
+          "locations": [
+            {
+              "location": "https://huggingface.co/mouseland/cellpose-sam/resolve/main/cpsam"
+            }
+          ]
+        }
+      }
+    }
+  },
+  "params": [
+    {
+      "name": "Segment Channel",
+      "arg_name": "segment_channel",
+      "value": 0,
+      "param_type": "channel",
+      "channel_start": 0,
+      "channel_start_label": "Grayscale",
+      "tooltip": "What channel to segment on. Cellpose-SAM is trained to be invariant to channel order and uses the first 3 channels of your image. Cellpose channel convention: 0=grayscale (no specific channel), 1=first image channel, 2=second image channel, etc. 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": "Resample",
+      "arg_name": "resample",
+      "value": true,
+      "tooltip": "Whether to run dynamics at original image size (rather than likely smaller resized image). Slower, but more accurate boundaries."
+    },
+    {
+      "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). Only used if do_3D is True."
+    },
+    {
+      "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."
+    },
+    {
+      "name": "Max size fraction",
+      "arg_name": "max_size_fraction",
+      "value": 0.4,
+      "tooltip": "Maximum size of ROIs as fraction of image size. Masks larger than this are removed."
+    },
+    {
+      "name": "Tile Overlap",
+      "arg_name": "tile_overlap",
+      "value": 0.1,
+      "tooltip": "Fraction of overlap of tiles when computing flows."
+    }
+  ]
+}