From 74ada9eb1068526066838cbbb3640f145408f6aa Mon Sep 17 00:00:00 2001 From: siemdejong <28396796+siemdejong@users.noreply.github.com> Date: Mon, 7 Sep 2026 15:04:29 +0200 Subject: [PATCH] add tia toolbox as path segmenter --- pyproject.toml | 16 +- run.py | 1 + segmenteer/__init__.py | 1 + segmenteer/methods/dl/__init__.py | 6 + segmenteer/methods/dl/tiatoolbox.py | 32 + uv.lock | 1466 ++++++++++++++++++++++++--- 6 files changed, 1389 insertions(+), 133 deletions(-) create mode 100644 segmenteer/methods/dl/tiatoolbox.py diff --git a/pyproject.toml b/pyproject.toml index fbf0856..93c3b59 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -154,6 +154,7 @@ all = [ "uvicorn[standard]>=0.32.0", "opencv-python-headless>=4.11.0.86", "histomicstk>=1.3.14", + "tiatoolbox>=2.1.3", ] dev = [ @@ -162,6 +163,9 @@ dev = [ histomicstk = [ "histomicstk>=1.3.14", ] +tiatoolbox = [ + "tiatoolbox>=2.1.3", +] [build-system] requires = ["uv_build>=0.9.26,<0.10.0"] @@ -171,8 +175,8 @@ build-backend = "uv_build" url = "https://girder.github.io/large_image_wheels" [[tool.uv.index]] -name = "pytorch-cu129" -url = "https://download.pytorch.org/whl/cu129" +name = "pytorch-cu126" +url = "https://download.pytorch.org/whl/cu126" explicit = true [tool.uv.build-backend] @@ -185,11 +189,12 @@ trident = { git = "https://github.com/mahmoodlab/trident.git", rev = "adf3b7e8fd tissue-segmentation = { git = "https://github.com/imi-bigpicture/tissue-segmentation.git", subdirectory = "tissue_segmentation", rev = "6d97a25a8255f591eb2c705611a32a5f56101a25"} sam-2 = { git = "https://github.com/facebookresearch/sam2.git", rev = "2b90b9f5ceec907a1c18123530e92e794ad901a4" } torch = [ - { index = "pytorch-cu129", marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { index = "pytorch-cu126", marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, ] torchvision = [ - { index = "pytorch-cu129", marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { index = "pytorch-cu126", marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, ] +tiatoolbox = { git = "https://github.com/TissueImageAnalytics/tiatoolbox", rev = "0482082c0934abf095b43cd60dd9b8db002755c5" } [tool.uv] index-strategy = "unsafe-best-match" @@ -201,6 +206,9 @@ exclude-dependencies = [ "tensorflow-cpu", "opencv-python", # ultralytics installs the wrong opencv package ] +override-dependencies = [ + { package = { name = "trident", version = "0.2.3" }, dependencies = ["timm>=1.0.3"] }, # It's very strict on an early timm version, while tiatoolbox requires >=1.0.3. +] [tool.uv.extra-build-dependencies] imagecodecs-numcodecs = ["imagecodecs", "numcodecs"] diff --git a/run.py b/run.py index eab0f07..e95336c 100644 --- a/run.py +++ b/run.py @@ -24,6 +24,7 @@ # ============================================================================= METHODS = [ + seg.TIAToolboxSegmenter(), seg.EntropyMaskerSegmenter(mpp=20), seg.BackgroundSubtractorMOG2Segmenter(mpp=20), seg.FESISegmenter(mpp=20), diff --git a/segmenteer/__init__.py b/segmenteer/__init__.py index bfdf76a..4b5c96d 100644 --- a/segmenteer/__init__.py +++ b/segmenteer/__init__.py @@ -128,6 +128,7 @@ "TRIDENTHESTSegmenter": ("segmenteer.methods.dl.trident", "TRIDENTHESTSegmenter"), "TRIDENTPathProfilerSegmenter": ("segmenteer.methods.dl.trident", "TRIDENTPathProfilerSegmenter"), "TRIDENTCPGSegmenter": ("segmenteer.methods.dl.trident", "TRIDENTCPGSegmenter"), + "TIAToolboxSegmenter": ("segmenteer.methods.dl.tiatoolbox", "TIAToolboxSegmenter"), } diff --git a/segmenteer/methods/dl/__init__.py b/segmenteer/methods/dl/__init__.py index b832daf..2c1515e 100644 --- a/segmenteer/methods/dl/__init__.py +++ b/segmenteer/methods/dl/__init__.py @@ -23,6 +23,11 @@ except ImportError: RTLucassenSlideSegmenter = None # type: ignore[assignment] +try: + from segmenteer.methods.dl.tiatoolbox import TIAToolboxSegmenter +except ImportError: + TIAToolboxSegmenter = None + try: from segmenteer.methods.dl.trident import ( TRIDENTGrandQCSegmenter, @@ -46,4 +51,5 @@ "BigPictureSegmenter", "TRIDENTPathProfilerSegmenter", "TRIDENTCPGSegmenter", + "TIAToolboxSegmenter", ] diff --git a/segmenteer/methods/dl/tiatoolbox.py b/segmenteer/methods/dl/tiatoolbox.py new file mode 100644 index 0000000..6fa4c6c --- /dev/null +++ b/segmenteer/methods/dl/tiatoolbox.py @@ -0,0 +1,32 @@ + # >>> from tiatoolbox.models.engine.semantic_segmentor import SemanticSegmentor + # >>> segmentor = SemanticSegmentor(model="efficientunet-tissue_mask") + # >>> results = segmentor.run( + # ... ["/example_wsi.svs"], + # ... masks=None, + # ... auto_get_mask=False, + # ... patch_mode=False, + # ... save_dir=Path("/tissue_mask/"), + # ... output_type="annotationstore", + # ... ) + +from tiatoolbox.models.engine.semantic_segmentor import SemanticSegmentor + +from segmenteer.core.base import PathSegmenter + +class TIAToolboxSegmenter(PathSegmenter): + def name() -> str: + return "tiatoolbox" + + def _segment_path(self, image_path, output_path): + segmentor = SemanticSegmentor(model="efficientunet-tissue_mask") + save_dir = output_path.parent / "output" + results = segmentor.run( + [image_path], + masks=None, + auto_get_mask=False, + patch_mode=False, + save_dir=save_dir, + output_type="dict", + device="cuda", + ) + print(results) \ No newline at end of file diff --git a/uv.lock b/uv.lock index 9f1e8ad..929e1e0 100644 --- a/uv.lock +++ b/uv.lock @@ -13,6 +13,7 @@ resolution-markers = [ ] [manifest] +overrides = [{ package = { name = "trident", version = "0.2.3" }, dependencies = 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== 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "tqdm" }, ] @@ -2886,9 +3796,9 @@ dependencies = [ { name = "safetensors" }, { name = "timm" }, { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 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"https://files.pythonhosted.org/packages/15/fa/d5a29d49240fb10bdead608b4d0c6805684a8f63b1f65863502be65b1ca4/segmentation_models_pytorch-0.5.0.tar.gz", hash = "sha256:cabba8aced6ef7bdcd6288dd9e1dc2840848aa819d539c455bd07aeceb2fdf96", size = 105150, upload-time = "2025-04-17T10:43:45.755Z" } @@ -2931,11 +3841,12 @@ all = [ { name = "segmentation-models-pytorch" }, { name = "slidesegmenter" }, { name = "tensorflow" }, + { name = "tiatoolbox" }, { name = "tissue-segmentation" }, { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "tqdm" }, { name = "trident" }, { name = "ultralytics" }, @@ -2959,9 +3870,9 @@ bigpicture = [ cpg = [ { name = "onnxruntime" }, { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "trident" }, ] dev = [ @@ -2977,9 +3888,9 @@ dl = [ { name = "tensorflow" }, { name = "tissue-segmentation" }, { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "tqdm" }, { name = "trident" }, { name = "ultralytics" }, @@ -2989,25 +3900,25 @@ entropymasker = [ ] fastsam = [ { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "ultralytics" }, ] grandqc = [ { name = "segmentation-models-pytorch" }, { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "tqdm" }, ] hest = [ { name = "huggingface-hub" }, { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, ] histomicstk = [ { name = "histomicstk" }, @@ -3022,9 +3933,9 @@ openslide = [ pathprofiler = [ { name = "huggingface-hub" }, { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "trident" }, ] rtlucassen = [ @@ -3038,17 +3949,20 @@ runtime = [ { name = "openslide-python" }, { name = "uvicorn", extra = ["standard"] }, ] +tiatoolbox = [ + { name = "tiatoolbox" }, +] torch = [ { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, ] trident = [ { name = "torch", version = "2.13.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torch", version = "2.13.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torch", version = "2.14.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "torchvision", version = "0.28.0", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux' and sys_platform != 'win32'" }, - { name = "torchvision", version = "0.28.0+cu129", source = { registry = "https://download.pytorch.org/whl/cu129" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, + { name = "torchvision", version = "0.29.0+cu126", source = { registry = "https://download.pytorch.org/whl/cu126" }, marker = "sys_platform == 'linux' or sys_platform == 'win32'" }, { name = "trident" }, ] wsi = [ @@ -3111,19 +4025,21 @@ requires-dist = [ { name = "tensorflow", marker = "extra == 'all'", specifier = ">=2.20.0,<2.21.0" }, { name = "tensorflow", marker = "extra == 'bigpicture'", specifier = ">=2.20.0,<2.21.0" }, { name = "tensorflow", marker = "extra == 'dl'", specifier = ">=2.20.0,<2.21.0" }, + { name = "tiatoolbox", marker = "extra == 'all'", git = "https://github.com/TissueImageAnalytics/tiatoolbox?rev=0482082c0934abf095b43cd60dd9b8db002755c5" }, + { name = "tiatoolbox", marker = "extra == 'tiatoolbox'", git = "https://github.com/TissueImageAnalytics/tiatoolbox?rev=0482082c0934abf095b43cd60dd9b8db002755c5" }, { name = "tifffile", specifier = ">=2025.5.10" }, { name = "tissue-segmentation", marker = "extra == 'all'", git = "https://github.com/imi-bigpicture/tissue-segmentation.git?subdirectory=tissue_segmentation&rev=6d97a25a8255f591eb2c705611a32a5f56101a25" }, { name = "tissue-segmentation", marker = "extra == 'bigpicture'", git = "https://github.com/imi-bigpicture/tissue-segmentation.git?subdirectory=tissue_segmentation&rev=6d97a25a8255f591eb2c705611a32a5f56101a25" }, { name = "tissue-segmentation", marker = "extra == 'dl'", git = 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name = "torch", marker = "(sys_platform == 'linux' and extra == 'all') or (sys_platform == 'win32' and extra == 'all')", specifier = ">=2.9.1", index = "https://download.pytorch.org/whl/cu126" }, + { name = "torch", marker = "(sys_platform == 'linux' and extra == 'cpg') or (sys_platform == 'win32' and extra == 'cpg')", specifier = ">=2.9.1", index = "https://download.pytorch.org/whl/cu126" }, + { name = "torch", marker = "(sys_platform == 'linux' and extra == 'dl') or (sys_platform == 'win32' and extra == 'dl')", specifier = ">=2.9.1", index = "https://download.pytorch.org/whl/cu126" }, + { name = "torch", marker = "(sys_platform == 'linux' and extra == 'fastsam') or (sys_platform == 'win32' and extra == 'fastsam')", specifier = ">=2.9.1", index = "https://download.pytorch.org/whl/cu126" }, + { name = "torch", marker = "(sys_platform == 'linux' and extra == 'grandqc') or (sys_platform == 'win32' and extra == 'grandqc')", specifier = ">=2.9.1", index = 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