Merge branch 'staging' into dev_roiset_coco

# Conflicts:
#	.gitignore
#	tests/base/test_roiset.py

.gitignore

-.idea/*
-*/.idea/*
 *__pycache__*
+
+# IDE profile files
+.idea/*
+
+# build and conda-build artifacts
+build/*
+dist/*
+*.egg-info/*
\ No newline at end of file

.idea/model_server.iml

 <?xml version="1.0" encoding="UTF-8"?>
 <module type="PYTHON_MODULE" version="4">
   <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$" />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/model_server" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/tests" isTestSource="false" />
+    </content>
     <orderEntry type="jdk" jdkName="Python 3.9 (model_server_env)" jdkType="Python SDK" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>

model_server/base/accessors.py

@@ -8,8 +8,8 @@ from skimage.io import imread, imsave
 import czifile
 import tifffile
 
-from model_server.base.process import make_rgb
-from model_server.base.process import is_mask
+from .process import make_rgb
+from .process import is_mask
 
 class GenericImageDataAccessor(ABC):
 

model_server/base/annotators.py

 import numpy as np
+from matplotlib import font_manager
 from PIL import Image, ImageDraw, ImageFont
 
-from model_server.base.process import rescale
+from .process import rescale
+
+def _get_font(font_size=18):
+    return ImageFont.truetype(
+        font_manager.findfont(
+            font_manager.FontProperties(
+                family='sans-serif',
+                weight='bold'
+            )
+        ),
+        size=font_size,
+    )
+
 
 def draw_boxes_on_3d_image(roiset, draw_full_depth=False, **kwargs):
     h, w, chroma, nz = roiset.acc_raw.shape
-    font_size = kwargs.get('font_size', 18)
     linewidth = kwargs.get('linewidth', 4)
 
     if ck := kwargs.get('channel'):
@@ -25,7 +37,7 @@ def draw_boxes_on_3d_image(roiset, draw_full_depth=False, **kwargs):
         for ci in range(0, len(channels)):
             pilimg = Image.fromarray(roiset.acc_raw.data[:, :, channels[ci], zi])
             draw = ImageDraw.Draw(pilimg)
-            draw.font = ImageFont.truetype(font="arial.ttf", size=font_size)
+            draw.font = _get_font()
 
             for roi in subset.itertuples('Roi'):
                 xm = round((roi.x0 + roi.x1) / 2)

model_server/base/api.py

 from fastapi import FastAPI, HTTPException
 from pydantic import BaseModel
 
-from model_server.base.models import DummyInstanceSegmentationModel, DummySemanticSegmentationModel
-from model_server.base.session import Session, InvalidPathError
-from model_server.base.validators import validate_workflow_inputs
-from model_server.base.workflows import classify_pixels
-from model_server.extensions.ilastik.workflows import infer_px_then_ob_model
+from .models import DummyInstanceSegmentationModel, DummySemanticSegmentationModel
+from .session import session, InvalidPathError
+from .validators import validate_workflow_inputs
+from .workflows import classify_pixels
 
 app = FastAPI(debug=True)
-session = Session()
 
-import model_server.extensions.ilastik.router
-app.include_router(model_server.extensions.ilastik.router.router)
+from ..extensions.ilastik.router import router as ilastik_router
+app.include_router(ilastik_router)
 
 @app.on_event("startup")
 def startup():

model_server/base/czi_util.py

@@ -5,7 +5,7 @@ import czifile
 import numpy as np
 import pandas as pd
 
-from model_server.base.accessors import InMemoryDataAccessor
+from .accessors import InMemoryDataAccessor
 
 
 def dump_czi_subblock_table(czif: czifile.CziFile, where: Path):

model_server/base/models.py

 from abc import ABC, abstractmethod
 from math import floor
-from typing import Union
 
 import numpy as np
 from pydantic import BaseModel
 
-from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, PatchStack
+from .accessors import GenericImageDataAccessor, InMemoryDataAccessor, PatchStack
 
 
 class Model(ABC):

model_server/base/roiset.py

@@ -14,12 +14,12 @@ from skimage.measure import label, regionprops_table, shannon_entropy, find_cont
 from sklearn.preprocessing import PolynomialFeatures
 from sklearn.linear_model import LinearRegression
 
-from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
-from model_server.base.models import InstanceSegmentationModel
-from model_server.base.process import get_safe_contours, pad, rescale, resample_to_8bit, make_rgb
-from model_server.base.annotators import draw_box_on_patch, draw_contours_on_patch, draw_boxes_on_3d_image
-from model_server.base.accessors import generate_file_accessor, PatchStack
-from model_server.base.process import mask_largest_object
+from .accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
+from .models import InstanceSegmentationModel
+from .process import get_safe_contours, pad, rescale, resample_to_8bit, make_rgb
+from .annotators import draw_box_on_patch, draw_contours_on_patch, draw_boxes_on_3d_image
+from .accessors import generate_file_accessor, PatchStack
+from .process import mask_largest_object
 
 
 class PatchParams(BaseModel):

model_server/base/session.py

 import logging
 import os
 
-from pathlib import Path
+from pathlib import Path, PureWindowsPath
 from pydantic import BaseModel
 from time import strftime, localtime
 from typing import Union
 
 import pandas as pd
 
-import model_server.conf.defaults
-from model_server.base.models import Model
+from ..conf import defaults
+from .models import Model
 
 logger = logging.getLogger(__name__)
 
 
-class Singleton(type):
-    _instances = {}
-
-    def __call__(cls, *args, **kwargs):
-        if cls not in cls._instances:
-            cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs)
-        return cls._instances[cls]
-
 class CsvTable(object):
     def __init__(self, fpath: Path):
         self.path = fpath
@@ -38,7 +30,7 @@ class CsvTable(object):
         self.empty = False
         return True
 
-class Session(object, metaclass=Singleton):
+class _Session(object):
     """
     Singleton class for a server session that persists data between API calls
     """
@@ -46,7 +38,6 @@ class Session(object, metaclass=Singleton):
     log_format = '%(asctime)s - %(levelname)s - %(message)s'
 
     def __init__(self, root: str = None):
-        print('Initializing session')
         self.models = {} # model_id : model object
         self.paths = self.make_paths(root)
 
@@ -97,13 +88,13 @@ class Session(object, metaclass=Singleton):
         :return: dictionary of session paths
         """
         if root is None:
-            root_path = Path(model_server.conf.defaults.root)
+            root_path = Path(defaults.root)
         else:
             root_path = Path(root)
-        sid = Session.create_session_id(root_path)
+        sid = _Session.create_session_id(root_path)
         paths = {'root': root_path}
         for pk in ['inbound_images', 'outbound_images', 'logs', 'tables']:
-            pa = root_path / sid / model_server.conf.defaults.subdirectories[pk]
+            pa = root_path / sid / defaults.subdirectories[pk]
             paths[pk] = pa
             try:
                 pa.mkdir(parents=True, exist_ok=True)
@@ -183,7 +174,7 @@ class Session(object, metaclass=Singleton):
         models = self.describe_loaded_models()
         for mid, det in models.items():
             if is_path:
-                if Path(det.get('params').get(key)) == Path(value):
+                if PureWindowsPath(det.get('params').get(key)).as_posix() == Path(value).as_posix():
                     return mid
             else:
                 if det.get('params').get(key) == value:
@@ -193,6 +184,11 @@ class Session(object, metaclass=Singleton):
     def restart(self, **kwargs):
         self.__init__(**kwargs)
 
+
+# create singleton instance
+session = _Session()
+
+
 class Error(Exception):
     pass
 

model_server/base/util.py

@@ -6,8 +6,8 @@ from typing import List
 
 import pandas as pd
 
-from model_server.base.accessors import InMemoryDataAccessor, write_accessor_data_to_file
-from model_server.base.models import Model
+from .accessors import InMemoryDataAccessor, write_accessor_data_to_file
+from .models import Model
 
 def autonumber_new_directory(where: str, prefix: str) -> str:
     """
@@ -163,4 +163,4 @@ def loop_workflow(
                 )
 
     if len(failures) > 0:
-        pd.DataFrame(failures).to_csv(Path(output_folder_path) / 'failures.csv')
\ No newline at end of file
+        pd.DataFrame(failures).to_csv(Path(output_folder_path) / 'failures.csv')

model_server/base/validators.py

 from fastapi import HTTPException
 
-from model_server.base.session import Session
-
-session = Session()
+from .session import session
 
 def validate_workflow_inputs(model_ids, inpaths):
     for mid in model_ids:

model_server/base/workflows.py

@@ -6,8 +6,8 @@ from pathlib import Path
 from time import perf_counter
 from typing import Dict
 
-from model_server.base.accessors import generate_file_accessor, write_accessor_data_to_file
-from model_server.base.models import SemanticSegmentationModel
+from .accessors import generate_file_accessor, write_accessor_data_to_file
+from .models import SemanticSegmentationModel
 
 from pydantic import BaseModel
 

model_server/conf/testing.py

+import json
+import os
+import unittest
+from multiprocessing import Process
 from pathlib import Path
 
-root = Path.home() / 'model_server' / 'testing'
-
-filename = 'D3-selection-01.czi'
-czifile = {
-    'filename': filename,
-    'path': root / filename,
-    'w': 1274,
-    'h': 1274,
-    'c': 5,
-    'z': 1,
-    'um_per_pixel': 1/3.9881,
-}
-
-filename = 'rgb.png'
-rgbpngfile = {
-    'filename': filename,
-    'path': root / filename,
-    'w': 64,
-    'h': 128,
-    'c': 3,
-    'z': 1
-}
-
-filename = 'mono.png'
-monopngfile = {
-    'filename': filename,
-    'path': root / filename,
-    'w': 64,
-    'h': 128,
-    'c': 1,
-    'z': 1
-}
-
-filename = 'zmask-test-stack.tif'
-tifffile = {
-    'filename': filename,
-    'path': root / filename,
-    'w': 512,
-    'h': 512,
-    'c': 2,
-    'z': 7,
-}
-
-filename = 'mono_zstack_mask.tif'
-monozstackmask = {
-    'filename': filename,
-    'path': root / filename,
-    'w': 256,
-    'h': 256,
-    'c': 1,
-    'z': 85
-}
-
-ilastik_classifiers = {
-    'px': root / 'ilastik' / 'demo_px.ilp',
-    'pxmap_to_obj': root / 'ilastik' / 'demo_obj.ilp',
-    'seg_to_obj': root / 'ilastik' / 'demo_obj_seg.ilp',
-    'px_color_zstack': root / 'ilastik' / 'px-3d-color.ilp',
-    'ob_pxmap_color_zstack': root / 'ilastik' / 'ob-pxmap-color-zstack.ilp',
-    'ob_seg_color_zstack': root / 'ilastik' / 'ob-seg-color-zstack.ilp',
-}
-
-roiset_test_data = {
-    'multichannel_zstack': {
-        'path': root / 'zmask-test-stack-chlorophyl.tif',
-        'w': 512,
-        'h': 512,
-        'c': 5,
-        'z': 7,
-        'mask_path': root / 'zmask-test-stack-mask.tif',
-        'mask_path_3d': root / 'zmask-test-stack-mask-3d.tif',
-    },
-    'pipeline_params': {
-        'segmentation_channel': 0,
-        'patches_channel': 4,
-        'pxmap_channel': 0,
-        'pxmap_threshold': 0.6,
-    },
-    'pixel_classifier': root / 'zmask' / 'AF405-bodies_boundaries.ilp',
-}
-
-output_path = root / 'testing_output'
-output_path.mkdir(parents=True, exist_ok=True)
\ No newline at end of file
+import requests
+from urllib3 import Retry
+
+
+class TestServerBaseClass(unittest.TestCase):
+    """
+    Base class for unittests of API functionality.  Implements both server and clients for testing.
+    """
+
+    app_name = 'model_server.base.api:app'
+
+    def setUp(self) -> None:
+        import uvicorn
+        host = '127.0.0.1'
+        port = 5001
+
+        self.server_process = Process(
+            target=uvicorn.run,
+            args=(self.app_name, ),
+            kwargs={'host': host, 'port': port, 'log_level': 'critical'},
+            daemon=True
+        )
+        self.uri = f'http://{host}:{port}/'
+        self.server_process.start()
+
+    def _get_sesh(self):
+        sesh = requests.Session()
+        retries = Retry(
+            total=5,
+            backoff_factor=0.1,
+        )
+        sesh.mount('http://', requests.adapters.HTTPAdapter(max_retries=retries))
+        return sesh
+
+    def _get(self, endpoint):
+        return self._get_sesh().get(self.uri + endpoint)
+
+    def _put(self, endpoint, query=None, body=None):
+        return self._get_sesh().put(
+            self.uri + endpoint,
+            params=query,
+            data=json.dumps(body)
+        )
+
+    def tearDown(self) -> None:
+        self.server_process.terminate()
+        self.server_process.join()
+
+
+def setup_test_data():
+    """
+    Look for test data, create test output directory, parse and return meta information
+    :return:
+        meta (dict) of test data and paths
+    """
+    # places to look for test data
+    data_paths = [
+        os.environ.get('UNITTEST_DATA_ROOT'),
+        Path.home() / 'model_server' / 'testing',
+        os.getcwd(),
+    ]
+    root = None
+
+    # look for first instance of summary.json
+    for dp in data_paths:
+        if dp is None:
+            continue
+        sf = (Path(dp) / 'summary.json')
+        if sf.exists():
+            with open(sf, 'r') as fh:
+                meta = json.load(fh)
+                root = dp
+                break
+
+    if root is None:
+        raise Exception('Could not find test data, try setting environmental variable UNITTEST_DATA_ROOT.')
+
+    meta['root'] = Path(root)
+    op_ev = os.environ.get('UNITTEST_OUTPUT', (meta['root'] / 'test_output'))
+    meta['output_path'] = Path(op_ev)
+    meta['output_path'].mkdir(parents=True, exist_ok=True)
+
+    # resolve relative paths
+    def _resolve_paths(d):
+        keys = list(d.keys())
+        for k in keys:
+            if k == 'name':
+                d['path'] = meta['root'] / d['name']
+            elif isinstance(d[k], dict):
+                _resolve_paths(d[k])
+    _resolve_paths(meta)
+
+    return meta
+
+# object containing test data paths and metadata, for import into unittest modules
+meta = setup_test_data()
\ No newline at end of file

model_server/extensions/ilastik/models.py

 import json
+from logging import getLogger
 import os
 from pathlib import Path
+import warnings
 
 import numpy as np
 from pydantic import BaseModel
-from skimage.filters import gaussian
 import vigra
 
 import model_server.extensions.ilastik.conf
-from model_server.base.accessors import PatchStack
-from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor
-from model_server.base.process import smooth
-from model_server.base.models import Model, ImageToImageModel, InstanceSegmentationModel, InvalidInputImageError, ParameterExpectedError, SemanticSegmentationModel
+from ...base.accessors import PatchStack
+from ...base.accessors import GenericImageDataAccessor, InMemoryDataAccessor
+from ...base.process import smooth
+from ...base.models import Model, ImageToImageModel, InstanceSegmentationModel, InvalidInputImageError, ParameterExpectedError, SemanticSegmentationModel
 
 class IlastikParams(BaseModel):
     project_file: str
@@ -44,8 +45,13 @@ class IlastikModel(Model):
         super().__init__(autoload, params)
 
     def load(self):
-        from ilastik import app
-        from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo
+        # suppress warnings when loading ilastik app
+        getLogger('ilastik.app').setLevel('ERROR')
+
+        with warnings.catch_warnings():
+            warnings.filterwarnings('ignore', category=DeprecationWarning)
+            from ilastik import app
+            from ilastik.applets.dataSelection.opDataSelection import PreloadedArrayDatasetInfo
 
         self.PreloadedArrayDatasetInfo = PreloadedArrayDatasetInfo
 

model_server/extensions/ilastik/router.py

 from fastapi import APIRouter, HTTPException
 
-from model_server.base.session import Session
-from model_server.base.validators import  validate_workflow_inputs
+from ...base.session import session
+from ...base.validators import validate_workflow_inputs
 
-from model_server.extensions.ilastik import models as ilm
-from model_server.base.models import ParameterExpectedError
-from model_server.extensions.ilastik.workflows import infer_px_then_ob_model
+from . import models as ilm
+from .workflows import infer_px_then_ob_model
 
 router = APIRouter(
     prefix='/ilastik',
     tags=['ilastik'],
 )
 
-session = Session()
-
 
 def load_ilastik_model(model_class: ilm.IlastikModel, params: ilm.IlastikParams) -> dict:
     """

model_server/extensions/ilastik/workflows.py

@@ -6,10 +6,9 @@ from typing import Dict
 
 from pydantic import BaseModel
 
-from model_server.extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
-from model_server.base.accessors import generate_file_accessor, write_accessor_data_to_file
-from model_server.base.workflows import Timer
-
+from .models import IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
+from ...base.accessors import generate_file_accessor, write_accessor_data_to_file
+from ...base.workflows import Timer
 
 class WorkflowRunRecord(BaseModel):
     pixel_model_id: str

model_server/scripts/run_server.py

@@ -6,7 +6,7 @@ from urllib3 import Retry
 import uvicorn
 import webbrowser
 
-from model_server.conf.defaults import server_conf
+from conf.defaults import server_conf
 
 def parse_args():
     parser = argparse.ArgumentParser(

model_server/scripts/verify_multichannel_ilastik_inputs.py

@@ -4,8 +4,8 @@ import h5py
 import numpy as np
 import pandas as pd
 
-from model_server.base.accessors import generate_file_accessor, write_accessor_data_to_file, InMemoryDataAccessor
-from model_server.extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
+from base.accessors import generate_file_accessor, write_accessor_data_to_file, InMemoryDataAccessor
+from extensions.ilastik.models import IlastikPixelClassifierModel, IlastikObjectClassifierFromPixelPredictionsModel
 
 def get_input_files(where_ilp: Path) -> list:
     files = []

pyproject.toml

@@ -2,15 +2,35 @@
 requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
+
 [project]
-name = "model_server_package_rhodes"
-version = "0.0.1"
+name = "model_server"
+license = {file = "LICENSE"}
+version = "2024.07.08"
 authors = [
   { name="Christopher Rhodes", email="christopher.rhodes@embl.de" },
 ]
 description = "Service for analyzing microscope images"
 readme = "README.md"
 requires-python = ">=3.9"
+dependencies = [
+  "czifile",
+  "fastapi >=0.101",
+  "ilastik ==1.4.1b15",
+  "imagecodecs",
+  "jupyterlab",
+  "matplotlib",
+  "numpy",
+  "pandas",
+  "pillow",
+  "pydantic ~=1.10.1",
+  "pytorch ==1.*",
+  "scikit-image >=0.21.0",
+  "scikit-learn >=1.5.0",
+  "tifffile",
+  "uvicorn >=0.23.0",
+  "zstd",
+]
 
 [project.urls]
 Homepage = "https://git.embl.de/rhodes/model_server"

requirements.yml

-name: model_server_env
-channels:
-  - pytorch
-  - ilastik-forge
-  - conda-forge
-  - defaults
-dependencies:
-  - affogato=0.3.3
-  - annotated-types=0.5.0
-  - anyio=3.7.1
-  - aom=3.5.0
-  - appdirs=1.4.4
-  - attrs=23.1.0
-  - bioimageio.core=0.5.8
-  - bioimageio.spec=0.4.9
-  - blas=2.118
-  - blas-devel=3.9.0
-  - blosc=1.21.5
-  - boost=1.74.0
-  - boost-cpp=1.74.0
-  - brotli=1.0.9
-  - brotli-bin=1.0.9
-  - brotli-python=1.0.9
-  - bzip2=1.0.8
-  - c-blosc2=2.10.2
-  - ca-certificates=2023.7.22
-  - cached-property=1.5.2
-  - cached_property=1.5.2
-  - cachetools=5.3.1
-  - cairo=1.16.0
-  - certifi=2023.7.22
-  - cfitsio=4.2.0
-  - charls=2.3.4
-  - charset-normalizer=3.2.0
-  - click=8.1.7
-  - colorama=0.4.6
-  - contourpy=1.1.0
-  - cycler=0.11.0
-  - czifile=2019.7.2
-  - dav1d=1.2.1
-  - dill=0.3.7
-  - dpct=1.2.post39
-  - et_xmlfile=1.1.0
-  - exceptiongroup=1.1.3
-  - expat=2.5.0
-  - fastapi=0.101.1
-  - fastfilters=0.2.4.post83
-  - fftw=3.3.10
-  - font-ttf-dejavu-sans-mono=2.37
-  - font-ttf-inconsolata=3.000
-  - font-ttf-source-code-pro=2.038
-  - font-ttf-ubuntu=0.83
-  - fontconfig=2.14.2
-  - fonts-conda-ecosystem=1
-  - fonts-conda-forge=1
-  - fonttools=4.42.1
-  - freetype=2.12.1
-  - fribidi=1.0.10
-  - fs=2.4.16
-  - future=0.18.3
-  - getopt-win32=0.1
-  - gettext=0.21.1
-  - giflib=5.2.1
-  - glib=2.78.0
-  - glib-tools=2.78.0
-  - glpk=5.0
-  - graphite2=1.3.13
-  - graphviz=8.1.0
-  - greenlet=2.0.2
-  - grpcio=1.41.1
-  - gst-plugins-base=1.22.5
-  - gstreamer=1.22.5
-  - gts=0.7.6
-  - h11=0.14.0
-  - h5py=3.8.0
-  - harfbuzz=6.0.0
-  - hdf5=1.12.2
-  - hytra=1.1.5
-  - icu=70.1
-  - idna=3.4
-  - ilastik=1.4.1b6
-  - ilastik-core=1.4.1b6
-  - ilastik-feature-selection=0.2.0
-  - ilastikrag=0.1.4
-  - ilastiktools=0.2.post37
-  - imagecodecs=2022.9.26
-  - imagecodecs-lite=2019.12.3
-  - imageio=2.31.1
-  - imath=3.1.6
-  - importlib-resources=6.0.1
-  - importlib_resources=6.0.1
-  - inferno=v0.4.2
-  - intel-openmp=2023.2.0
-  - joblib=1.3.2
-  - jpeg=9e
-  - jsonschema=4.19.0
-  - jsonschema-specifications=2023.7.1
-  - jxrlib=1.1
-  - kiwisolver=1.4.5
-  - krb5=1.20.1
-  - lazy_loader=0.3
-  - lcms2=2.14
-  - lemon=1.3.1
-  - lerc=4.0.0
-  - libabseil=20230802.0
-  - libaec=1.0.6
-  - libavif=0.11.1
-  - libblas=3.9.0
-  - libbrotlicommon=1.0.9
-  - libbrotlidec=1.0.9
-  - libbrotlienc=1.0.9
-  - libcblas=3.9.0
-  - libclang=15.0.7
-  - libclang13=15.0.7
-  - libcurl=8.1.2
-  - libdeflate=1.14
-  - libexpat=2.5.0
-  - libffi=3.4.2
-  - libgd=2.3.3
-  - libglib=2.78.0
-  - libhwloc=2.9.2
-  - libiconv=1.17
-  - liblapack=3.9.0
-  - liblapacke=3.9.0
-  - libogg=1.3.4
-  - libpng=1.6.39
-  - libprotobuf=4.23.4
-  - libsqlite=3.43.0
-  - libssh2=1.11.0
-  - libtiff=4.4.0
-  - libuv=1.44.2
-  - libvorbis=1.3.7
-  - libwebp=1.3.1
-  - libwebp-base=1.3.1
-  - libxcb=1.13
-  - libxml2=2.11.5
-  - libzlib=1.2.13
-  - libzopfli=1.0.3
-  - llvmlite=0.40.1
-  - lz4-c=1.9.4
-  - m2w64-gcc-libgfortran=5.3.0
-  - m2w64-gcc-libs=5.3.0
-  - m2w64-gcc-libs-core=5.3.0
-  - m2w64-gmp=6.1.0
-  - m2w64-libwinpthread-git=5.0.0.4634.697f757
-  - mamutexport=0.2.1.post6
-  - marching_cubes=0.3.post9
-  - markdown-it-py=3.0.0
-  - marshmallow=3.20.1
-  - marshmallow-jsonschema=0.13.0
-  - marshmallow-union=0.1.15.post1
-  - matplotlib-base=3.7.2
-  - mdurl=0.1.0
-  - mkl=2022.1.0
-  - mkl-devel=2022.1.0
-  - mkl-include=2022.1.0
-  - mrcfile=1.4.3
-  - msys2-conda-epoch=20160418
-  - munkres=1.1.4
-  - ndstructs=0.0.5dev0
-  - networkx=3.1
-  - nifty=1.2.1
-  - numba=0.57.1
-  - numpy=1.22.4
-  - openexr=3.1.5
-  - openjpeg=2.5.0
-  - openpyxl=3.1.2
-  - openssl=3.1.2
-  - packaging=23.1
-  - pandas=1.5.3
-  - pango=1.50.14
-  - pcre2=10.40
-  - pillow=9.2.0
-  - pip=23.2.1
-  - pixman=0.40.0
-  - pkgutil-resolve-name=1.3.10
-  - platformdirs=3.10.0
-  - ply=3.11
-  - pooch=1.7.0
-  - protobuf=4.23.4
-  - psutil=5.9.5
-  - pthread-stubs=0.4
-  - pthreads-win32=2.9.1
-  - pydantic=1.10.2
-  - pydantic-core=2.6.3
-  - pygments=2.16.1
-  - pyopengl=3.1.6
-  - pyparsing=3.0.9
-  - pyqt=5.15.9
-  - pyqt5-sip=12.12.2
-  - pyqtgraph=0.13.3
-  - pysocks=1.7.1
-  - python=3.9.18
-  - python-dateutil=2.8.2
-  - python-elf=0.4.7
-  - python-stdnum=1.19
-  - python_abi=3.9
-  - pytorch=1.13.1
-  - pytorch-mutex=1.0
-  - pytz=2023.3.post1
-  - pywavelets=1.4.1
-  - pyyaml=6.0.1
-  - qimage2ndarray=1.8.3
-  - qt-main=5.15.8
-  - referencing=0.30.2
-  - requests=2.31.0
-  - rich=13.5.1
-  - rpds-py=0.10.2
-  - ruamel.yaml=0.17.32
-  - ruamel.yaml.clib=0.2.7
-  - scikit-image=0.21.0
-  - scikit-learn=1.3.0
-  - scipy=1.11.2
-  - setuptools=68.1.2
-  - shellingham=1.5.3
-  - sip=6.7.11
-  - six=1.16.0
-  - skan=0.11.0
-  - snappy=1.1.10
-  - sniffio=1.3.0
-  - starlette=0.27.0
-  - tbb=2021.10.0
-  - tensorboardx=2.6.2.2
-  - threadpoolctl=3.2.0
-  - tifffile=2022.10.10
-  - tiktorch=23.6.0
-  - tk=8.6.12
-  - toml=0.10.2
-  - tomli=2.0.1
-  - toolz=0.12.0
-  - torchvision=0.14.1
-  - tqdm=4.66.1
-  - typer=0.9.0
-  - typing-extensions=4.7.1
-  - typing_extensions=4.7.1
-  - tzdata=2023c
-  - ucrt=10.0.22621.0
-  - unicodedata2=15.0.0
-  - urllib3=2.0.4
-  - uvicorn=0.23.2
-  - vc=14.3
-  - vc14_runtime=14.36.32532
-  - vigra=1.11.1
-  - volumina=1.3.10
-  - vs2015_runtime=14.36.32532
-  - wheel=0.41.2
-  - win_inet_pton=1.1.0
-  - xarray=2023.8.0
-  - xorg-kbproto=1.0.7
-  - xorg-libice=1.0.10
-  - xorg-libsm=1.2.3
-  - xorg-libx11=1.8.4
-  - xorg-libxau=1.0.11
-  - xorg-libxdmcp=1.1.3
-  - xorg-libxext=1.3.4
-  - xorg-libxpm=3.5.16
-  - xorg-libxt=1.3.0
-  - xorg-xextproto=7.3.0
-  - xorg-xproto=7.0.31
-  - xz=5.2.6
-  - yaml=0.2.5
-  - yapsy=1.12.2
-  - z5py=2.0.16
-  - zfp=1.0.0
-  - zipp=3.16.2
-  - zlib=1.2.13
-  - zlib-ng=2.0.7
-  - zstd=1.5.5
-  - pip:
-      - build==1.0.3
-      - importlib-metadata==7.0.0
-      - pyproject-hooks==1.0.0