micro-sam 1.8.0__tar.gz

micro_sam-1.8.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Computational Cell Analytics (Research Group of Prof. Dr. Constantin Pape)
+
+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.

micro_sam-1.8.0/MANIFEST.in

@@ -0,0 +1,5 @@
+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

micro_sam-1.8.0/PKG-INFO

@@ -0,0 +1,123 @@
+Metadata-Version: 2.4
+Name: micro-sam
+Version: 1.8.0
+Summary: Segment Anything For Microscopy
+Home-page: https://github.com/computational-cell-analytics/micro-sam
+Author: Anwai Archit, Paul Hilt, Genevieve Buckley, Constantin Pape
+License: MIT
+Project-URL: Bug Tracker, https://github.com/computational-cell-analytics/micro-sam/issues
+Project-URL: Documentation, https://computational-cell-analytics.github.io/micro-sam/micro_sam.html
+Project-URL: Source Code, https://github.com/computational-cell-analytics/micro-sam
+Project-URL: User Support, https://github.com/computational-cell-analytics/micro-sam/issues
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: bioimage-cpp>=0.3
+Requires-Dist: bioimageio.core
+Requires-Dist: h5py
+Requires-Dist: imagecodecs
+Requires-Dist: imageio
+Requires-Dist: joblib
+Requires-Dist: kornia
+Requires-Dist: magicgui
+Requires-Dist: matplotlib
+Requires-Dist: napari<0.7
+Requires-Dist: natsort
+Requires-Dist: networkx
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pooch
+Requires-Dist: PyQt5
+Requires-Dist: python-elf>=0.9
+Requires-Dist: scikit-image
+Requires-Dist: scikit-learn
+Requires-Dist: segment-anything
+Requires-Dist: superqt
+Requires-Dist: timm
+Requires-Dist: torch>=2.5
+Requires-Dist: torch-em>=0.9
+Requires-Dist: torchvision
+Requires-Dist: tqdm
+Requires-Dist: trackastra>=0.5.3
+Requires-Dist: xarray
+Requires-Dist: xxhash
+Requires-Dist: zarr
+Dynamic: license-file
+
+[![DOC](https://shields.mitmproxy.org/badge/docs-pdoc.dev-brightgreen.svg)](https://computational-cell-analytics.github.io/micro-sam/)
+[![Conda](https://anaconda.org/conda-forge/micro_sam/badges/version.svg)](https://anaconda.org/conda-forge/micro_sam)
+[![codecov](https://codecov.io/gh/computational-cell-analytics/micro-sam/graph/badge.svg?token=7ETPP5CABP)](https://codecov.io/gh/computational-cell-analytics/micro-sam)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7919746.svg)](https://doi.org/10.5281/zenodo.7919746)
+
+# Segment Anything for Microscopy
+
+<a href="https://github.com/computational-cell-analytics/micro-sam"><img src="https://github.com/computational-cell-analytics/micro-sam/blob/main/doc/logo/logo_and_text.png" width="300" align="right">
+
+Tools for segmentation and tracking in microscopy build on top of [Segment Anything](https://segment-anything.com/).
+Segment and track objects in microscopy images interactively with a few clicks!
+
+We implement napari applications for:
+- interactive 2d segmentation (Left: interactive cell segmentation)
+- interactive 3d segmentation (Middle: interactive mitochondria segmentation in EM)
+- interactive tracking of 2d image data (Right: interactive cell tracking)
+
+<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/d04cb158-9f5b-4460-98cd-023c4f19cccd" width="256">
+<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/dfca3d9b-dba5-440b-b0f9-72a0683ac410" width="256">
+<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/aefbf99f-e73a-4125-bb49-2e6592367a64" width="256">
+
+If you run into any problems or have questions regarding our tool please open an [issue](https://github.com/computational-cell-analytics/micro-sam/issues/new/choose) on Github or reach out via [image.sc](https://forum.image.sc/) using the tag `micro-sam`, and tagging [@constantinpape](https://forum.image.sc/u/constantinpape/summary) and [@anwai98](https://forum.image.sc/u/anwai98/summary).
+You can follow recent updates on `micro_sam` in our [news feed](https://forum.image.sc/t/microsam-news-feed).
+
+## Installation and Usage
+
+Please check [the documentation](https://computational-cell-analytics.github.io/micro-sam/) for details on how to install and use `micro_sam`. You can also watch [the quickstart video](https://youtu.be/gcv0fa84mCc), [our virtual I2K workshop video](https://www.youtube.com/watch?v=dxjU4W7bCis&list=PLdA9Vgd1gxTbvxmtk9CASftUOl_XItjDN&index=33) or [all video tutorials](https://youtube.com/playlist?list=PLwYZXQJ3f36GQPpKCrSbHjGiH39X4XjSO&si=qNbB8IFXqAX33r_Z).
+
+
+## Contributing
+
+We welcome new contributions!
+
+If you are interested in contributing to `micro-sam`, please see the [contributing guide](https://computational-cell-analytics.github.io/micro-sam/micro_sam.html#contribution-guide). The first step is to [discuss your idea in a new issue](https://github.com/computational-cell-analytics/micro-sam/issues/new) with the current developers.
+
+
+## Citation
+
+If you are using this repository in your research please cite
+- our [paper](https://www.nature.com/articles/s41592-024-02580-4) (now published in Nature Methods!)
+- and the original [Segment Anything publication](https://arxiv.org/abs/2304.02643).
+- If you use `vit-tiny` models please also cite [Mobile SAM](https://arxiv.org/abs/2306.14289).
+- If you use automatic tracking, please also cite [Trackastra](https://arxiv.org/abs/2405.15700).
+
+
+## Related Projects
+
+There are a few other napari plugins build around Segment Anything:
+- https://github.com/MIC-DKFZ/napari-sam (2d and 3d support)
+- https://github.com/royerlab/napari-segment-anything (only 2d support)
+- https://github.com/hiroalchem/napari-SAM4IS
+
+Compared to these we support more applications (2d, 3d and tracking), and provide finetuning methods and finetuned models for microscopy data.
+[WebKnossos](https://webknossos.org/) and [QuPath](https://qupath.github.io/) also offer integration of Segment Anything for interactive segmentation.
+
+We have also built follow-up work that is based on `micro_sam`:
+- https://github.com/computational-cell-analytics/patho-sam - improves SAM for histopathology.
+- https://github.com/computational-cell-analytics/medico-sam - improves SAM for medical imaging.
+- https://github.com/computational-cell-analytics/peft-sam - studies parameter efficient fine-tuning for SAM.
+
+## Release Overview
+
+You can find an overview of changes introduced in previous releases [here](https://github.com/computational-cell-analytics/micro-sam/blob/main/RELEASE_OVERVIEW.md).

micro_sam-1.8.0/README.md

@@ -0,0 +1,63 @@
+[![DOC](https://shields.mitmproxy.org/badge/docs-pdoc.dev-brightgreen.svg)](https://computational-cell-analytics.github.io/micro-sam/)
+[![Conda](https://anaconda.org/conda-forge/micro_sam/badges/version.svg)](https://anaconda.org/conda-forge/micro_sam)
+[![codecov](https://codecov.io/gh/computational-cell-analytics/micro-sam/graph/badge.svg?token=7ETPP5CABP)](https://codecov.io/gh/computational-cell-analytics/micro-sam)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7919746.svg)](https://doi.org/10.5281/zenodo.7919746)
+
+# Segment Anything for Microscopy
+
+<a href="https://github.com/computational-cell-analytics/micro-sam"><img src="https://github.com/computational-cell-analytics/micro-sam/blob/main/doc/logo/logo_and_text.png" width="300" align="right">
+
+Tools for segmentation and tracking in microscopy build on top of [Segment Anything](https://segment-anything.com/).
+Segment and track objects in microscopy images interactively with a few clicks!
+
+We implement napari applications for:
+- interactive 2d segmentation (Left: interactive cell segmentation)
+- interactive 3d segmentation (Middle: interactive mitochondria segmentation in EM)
+- interactive tracking of 2d image data (Right: interactive cell tracking)
+
+<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/d04cb158-9f5b-4460-98cd-023c4f19cccd" width="256">
+<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/dfca3d9b-dba5-440b-b0f9-72a0683ac410" width="256">
+<img src="https://github.com/computational-cell-analytics/micro-sam/assets/4263537/aefbf99f-e73a-4125-bb49-2e6592367a64" width="256">
+
+If you run into any problems or have questions regarding our tool please open an [issue](https://github.com/computational-cell-analytics/micro-sam/issues/new/choose) on Github or reach out via [image.sc](https://forum.image.sc/) using the tag `micro-sam`, and tagging [@constantinpape](https://forum.image.sc/u/constantinpape/summary) and [@anwai98](https://forum.image.sc/u/anwai98/summary).
+You can follow recent updates on `micro_sam` in our [news feed](https://forum.image.sc/t/microsam-news-feed).
+
+## Installation and Usage
+
+Please check [the documentation](https://computational-cell-analytics.github.io/micro-sam/) for details on how to install and use `micro_sam`. You can also watch [the quickstart video](https://youtu.be/gcv0fa84mCc), [our virtual I2K workshop video](https://www.youtube.com/watch?v=dxjU4W7bCis&list=PLdA9Vgd1gxTbvxmtk9CASftUOl_XItjDN&index=33) or [all video tutorials](https://youtube.com/playlist?list=PLwYZXQJ3f36GQPpKCrSbHjGiH39X4XjSO&si=qNbB8IFXqAX33r_Z).
+
+
+## Contributing
+
+We welcome new contributions!
+
+If you are interested in contributing to `micro-sam`, please see the [contributing guide](https://computational-cell-analytics.github.io/micro-sam/micro_sam.html#contribution-guide). The first step is to [discuss your idea in a new issue](https://github.com/computational-cell-analytics/micro-sam/issues/new) with the current developers.
+
+
+## Citation
+
+If you are using this repository in your research please cite
+- our [paper](https://www.nature.com/articles/s41592-024-02580-4) (now published in Nature Methods!)
+- and the original [Segment Anything publication](https://arxiv.org/abs/2304.02643).
+- If you use `vit-tiny` models please also cite [Mobile SAM](https://arxiv.org/abs/2306.14289).
+- If you use automatic tracking, please also cite [Trackastra](https://arxiv.org/abs/2405.15700).
+
+
+## Related Projects
+
+There are a few other napari plugins build around Segment Anything:
+- https://github.com/MIC-DKFZ/napari-sam (2d and 3d support)
+- https://github.com/royerlab/napari-segment-anything (only 2d support)
+- https://github.com/hiroalchem/napari-SAM4IS
+
+Compared to these we support more applications (2d, 3d and tracking), and provide finetuning methods and finetuned models for microscopy data.
+[WebKnossos](https://webknossos.org/) and [QuPath](https://qupath.github.io/) also offer integration of Segment Anything for interactive segmentation.
+
+We have also built follow-up work that is based on `micro_sam`:
+- https://github.com/computational-cell-analytics/patho-sam - improves SAM for histopathology.
+- https://github.com/computational-cell-analytics/medico-sam - improves SAM for medical imaging.
+- https://github.com/computational-cell-analytics/peft-sam - studies parameter efficient fine-tuning for SAM.
+
+## Release Overview
+
+You can find an overview of changes introduced in previous releases [here](https://github.com/computational-cell-analytics/micro-sam/blob/main/RELEASE_OVERVIEW.md).

micro_sam-1.8.0/micro_sam/__init__.py

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+"""
+.. include:: ../doc/start_page.md
+.. include:: ../doc/installation.md
+.. include:: ../doc/annotation_tools.md
+.. include:: ../doc/cli_tools.md
+.. include:: ../doc/python_library.md
+.. include:: ../doc/finetuned_models.md
+.. include:: ../doc/apg.md
+.. include:: ../doc/data_submission.md
+.. include:: ../doc/faq.md
+.. include:: ../doc/contributing.md
+.. include:: ../doc/band.md
+"""
+
+import os
+
+from .__version__ import __version__
+
+os.environ["PYTORCH_ENABLE_MPS_FALLBACK"] = "1"

micro_sam-1.8.0/micro_sam/__version__.py

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+__version__ = "1.8.0"

micro_sam-1.8.0/micro_sam/_model_settings.py

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+# The settings for the instance segmentation widget with ais.
+AIS_SETTINGS = {
+    "vit_t_lm": {
+        "center_distance_thresh": 0.5,
+        "boundary_distance_thresh": 0.5,
+        "distance_smoothing": 2.0,
+        "min_size": 100,
+    },
+    "vit_b_lm": {
+        "center_distance_thresh": 0.4,
+        "boundary_distance_thresh": 0.5,
+        "distance_smoothing": 2.0,
+        "min_size": 100,
+    },
+    "vit_l_lm": {
+        "center_distance_thresh": 0.4,
+        "boundary_distance_thresh": 0.4,
+        "distance_smoothing": 1.6,
+        "min_size": 100,
+    },
+    "vit_h_lm": {
+        "center_distance_thresh": 0.5,
+        "boundary_distance_thresh": 0.5,
+        "distance_smoothing": 1.4,
+        "min_size": 100,
+    },
+
+    "vit_t_em_organelles": {
+        "center_distance_thresh": 0.4,
+        "boundary_distance_thresh": 0.5,
+        "distance_smoothing": 1.2,
+        "min_size": 100,
+    },
+    "vit_b_em_organelles": {
+        "center_distance_thresh": 0.3,
+        "boundary_distance_thresh": 0.4,
+        "distance_smoothing": 1.2,
+        "min_size": 100,
+    },
+    "vit_l_em_organelles": {
+        "center_distance_thresh": 0.3,
+        "boundary_distance_thresh": 0.4,
+        "distance_smoothing": 1.2,
+        "min_size": 100,
+    },
+    "vit_h_em_organelles": {
+        "center_distance_thresh": 0.3,
+        "boundary_distance_thresh": 0.4,
+        "distance_smoothing": 1.2,
+        "min_size": 100,
+    }
+}
+
+# The settings for the instance segmentation widget with amg.
+AMG_SETTINGS = {
+    "vit_t_lm": {
+        "pred_iou_thresh": 0.6,
+        "stability_score_thresh": 0.65,
+        "min_object_size": 100,
+    },
+    "vit_b_lm": {
+        "pred_iou_thresh": 0.65,
+        "stability_score_thresh": 0.7,
+        "min_object_size": 100,
+    },
+    "vit_l_lm": {
+        "pred_iou_thresh": 0.65,
+        "stability_score_thresh": 0.73,
+        "min_object_size": 100,
+    },
+    "vit_h_lm": {
+        "pred_iou_thresh": 0.65,
+        "stability_score_thresh": 0.7,
+        "min_object_size": 100,
+    },
+
+    "vit_t_em_organelles": {
+        "pred_iou_thresh": 0.75,
+        "stability_score_thresh": 0.75,
+        "min_object_size": 100,
+    },
+    "vit_b_em_organelles": {
+        "pred_iou_thresh": 0.75,
+        "stability_score_thresh": 0.75,
+        "min_object_size": 100,
+    },
+    "vit_l_em_organelles": {
+        "pred_iou_thresh": 0.8,
+        "stability_score_thresh": 0.8,
+        "min_object_size": 100,
+    },
+    "vit_h_em_organelles": {
+        "pred_iou_thresh": 0.8,
+        "stability_score_thresh": 0.8,
+        "min_object_size": 100,
+    },
+}
+
+# The settings for the nd segment widget.
+ND_SEGMENT_SETTINGS = {
+    "vit_t_lm": {
+        "projection_mode": "box",
+        "iou_threshold": 0.8,
+        "box_extension": 0.025,
+    },
+    "vit_b_lm": {
+        "projection_mode": "box",
+        "iou_threshold": 0.8,
+        "box_extension": 0.025,
+    },
+    "vit_l_lm": {
+        "projection_mode": "box",
+        "iou_threshold": 0.8,
+        "box_extension": 0.025,
+    },
+    "vit_h_lm": {
+        "projection_mode": "box",
+        "iou_threshold": 0.8,
+        "box_extension": 0.0025,
+    },
+
+    "vit_t_em_organelles": {
+        "projection_mode": "single_point",
+        "iou_threshold": 0.6,
+        "box_extension": 0.025,
+    },
+    "vit_b_em_organelles": {
+        "projection_mode": "single_point",
+        "iou_threshold": 0.6,
+        "box_extension": 0.025,
+    },
+    "vit_l_em_organelles": {
+        "projection_mode": "single_point",
+        "iou_threshold": 0.6,
+        "box_extension": 0.025,
+    },
+    "vit_h_em_organelles": {
+        "projection_mode": "single_point",
+        "iou_threshold": 0.6,
+        "box_extension": 0.025,
+    }
+}

micro_sam-1.8.0/micro_sam/_test_util.py

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+import numpy as np
+
+
+def check_layer_initialization(viewer, expected_shape):
+    """Utility function to check the initial layer setup is correct."""
+
+    assert len(viewer.layers) == 6
+    expected_layer_names = [
+        "image", "auto_segmentation", "committed_objects", "current_object", "point_prompts", "prompts"
+    ]
+
+    for layer_name in expected_layer_names:
+        assert layer_name in viewer.layers
+
+    # Check prompt layers
+    assert viewer.layers["prompts"].data == []  # shape data is list, not numpy array
+    np.testing.assert_equal(viewer.layers["point_prompts"].data, 0)
+
+    # Check segmentation layers.
+    for layer_name in ["auto_segmentation", "committed_objects", "current_object"]:
+        assert viewer.layers[layer_name].data.shape == expected_shape
+        np.testing.assert_equal(viewer.layers[layer_name].data, 0)

micro_sam-1.8.0/micro_sam/_vendored.py

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+"""Functions from other third party libraries.
+
+We can remove these functions once the bugs affecting our code is fixed upstream.
+
+The license type of the thrid party software project must be compatible with
+the software license the micro-sam project is distributed under.
+"""
+
+from typing import Any, Dict, List, Literal
+
+import numpy as np
+
+import torch
+
+try:
+    from numba import njit
+    HAVE_NUMBA = True
+except (ImportError, SystemError):
+    HAVE_NUMBA = False
+
+    def njit(func):
+        return func
+
+from bioimage_cpp.utils import compute_rle as _compute_rle_cpp
+
+
+def _compute_rle_bioimage_cpp(mask):
+    # bioimage-cpp returns an int64 numpy array; convert to a list to match the
+    # numpy/numba implementations and the COCO/SAM RLE format.
+    return _compute_rle_cpp(mask).tolist()
+
+
+def batched_mask_to_box(masks: torch.Tensor) -> torch.Tensor:
+    """Calculates boxes in XYXY format around masks. Return [0, 0, 0, 0] for an empty mask.
+
+    For input shape C1xC2x...xHxW, the output shape is C1xC2x...x4.
+
+    This function is adapted from https://github.com/facebookresearch/segment-anything/segment_anything/util/amg.py
+    so that it also supports tensors that have MPS device.
+    It further ensures that inputs are boolean tensors, otherwise the function yields wrong results.
+    See https://github.com/facebookresearch/segment-anything/issues/552 for details.
+    """
+    assert masks.dtype == torch.bool, masks.dtype
+
+    # torch.max below raises an error on empty inputs, just skip in this case
+    if torch.numel(masks) == 0:
+        return torch.zeros(*masks.shape[:-2], 4, device=masks.device)
+
+    # Normalize shape to CxHxW
+    shape = masks.shape
+    h, w = shape[-2:]
+    if len(shape) > 2:
+        masks = masks.flatten(0, -3)
+    else:
+        masks = masks.unsqueeze(0)
+
+    # Get top and bottom edges
+    in_height, _ = torch.max(masks, dim=-1)
+    in_height_coords = in_height * torch.arange(h, dtype=torch.int, device=in_height.device)[None, :]
+    bottom_edges, _ = torch.max(in_height_coords, dim=-1)
+    in_height_coords = in_height_coords + h * (~in_height)
+    in_height_coords = in_height_coords.type(torch.int)
+    top_edges, _ = torch.min(in_height_coords, dim=-1)
+
+    # Get left and right edges
+    in_width, _ = torch.max(masks, dim=-2)
+    in_width_coords = in_width * torch.arange(w, dtype=torch.int, device=in_width.device)[None, :]
+    right_edges, _ = torch.max(in_width_coords, dim=-1)
+    in_width_coords = in_width_coords + w * (~in_width)
+    in_width_coords = in_width_coords.type(torch.int)
+    left_edges, _ = torch.min(in_width_coords, dim=-1)
+
+    # If the mask is empty the right edge will be to the left of the left edge.
+    # Replace these boxes with [0, 0, 0, 0]
+    empty_filter = (right_edges < left_edges) | (bottom_edges < top_edges)
+    out = torch.stack([left_edges, top_edges, right_edges, bottom_edges], dim=-1)
+    out = out * (~empty_filter).unsqueeze(-1)
+
+    # Return to original shape
+    if len(shape) > 2:
+        out = out.reshape(*shape[:-2], 4)
+    else:
+        out = out[0]
+
+    return out
+
+
+@njit
+def _compute_rle_numba(mask):
+    val = mask[0]
+    counts = [int(x) for x in range(0)] if val == 0 else [0]
+    count = 0
+    for m in mask:
+        if val == m:
+            count += 1
+        else:
+            val = m
+            counts.append(count)
+            count = 1
+    counts.append(count)
+    return counts
+
+
+def _compute_rle_numpy(mask):
+    diffs = mask[1:] != mask[:-1]  # pairwise unequal (string safe)
+    indices = np.append(np.where(diffs), len(mask) - 1)  # must include last element position
+    # count needs to start with 0 if the mask begins with 1
+    counts = [] if mask[0] == 0 else [0]
+    # compute the actual RLE
+    counts += np.diff(np.append(-1, indices)).tolist()
+    return counts
+
+
+def mask_to_rle_pytorch(
+    tensor: torch.Tensor, rle_implementation: Literal["default", "numpy", "numba", "bioimage_cpp"] = "default"
+) -> List[Dict[str, Any]]:
+    """Calculates the runlength encoding of binary input masks.
+
+    This replaces the function in
+    https://github.com/facebookresearch/segment-anything/segment_anything/util/amg.py
+    with a version that computes the RLE purely on the CPU.
+    This does not lead to any performance deficits when running on the GPU, but it speeds the computation
+    up significantly compared to running this on an MPS device.
+    The RLE implementation is based on
+    https://stackoverflow.com/questions/1066758/find-length-of-sequences-of-identical-values-in-a-numpy-array-run-length-encodi
+    """
+    # Put in fortran order and flatten h, w
+    b, h, w = tensor.shape
+    tensor = tensor.permute(0, 2, 1).flatten(1)
+    tensor = tensor.detach().cpu().numpy()
+
+    if rle_implementation == "default":
+        rle_implementation = "bioimage_cpp"
+
+    if rle_implementation == "numba":
+        assert HAVE_NUMBA
+        rle_impl = _compute_rle_numba
+    elif rle_implementation == "numpy":
+        rle_impl = _compute_rle_numpy
+    elif rle_implementation == "bioimage_cpp":
+        rle_impl = _compute_rle_bioimage_cpp
+    else:
+        raise ValueError(
+            f"RLE implementation {rle_implementation} is not available. "
+            "Has to be one of 'numpy', 'numba' or 'bioimage_cpp'."
+        )
+
+    out = []
+    for mask in tensor:
+        counts = rle_impl(mask)
+        out.append({"size": [h, w], "counts": counts})
+    return out