Merge pull request #40 from fmi-faim/cellpose

.github/workflows/test.yml

@@ -26,7 +26,7 @@ jobs:
  fail-fast: false
  matrix:
  os: [ubuntu-latest, windows-latest, macos-latest]
- python-version: ['3.7', '3.8', '3.9', '3.10', '3.11.0-beta.5 - 3.11']
+ python-version: ['3.8', '3.9', '3.10', '3.11']
 
  steps:
  - uses: actions/checkout@v3

config_cellpose.yml

@@ -0,0 +1,18 @@
+# SPDX-FileCopyrightText: 2023 Friedrich Miescher Institute for Biomedical Research (FMI), Basel (Switzerland)
+#
+# SPDX-License-Identifier: MIT
+
+# Required
+file_selection: # criteria for file selection in case of multiple channels/slices per position
+ channel: C01
+process: # choose method how to segment, filter, and sample the objects
+ segment: cellpose
+ filter: []
+ sample: centers
+
+# Each subsequent section provides arguments to one of the methods defined in 'process'
+cellpose:
+ diameter: 10.0
+ pretrained_model: cyto2
+ cellprob_threshold: 0.0
+ flow_threshold: 0.4

pyproject.toml

@@ -10,7 +10,7 @@ build-backend = "hatchling.build"
 name = "faim-wako-searchfirst"
 description = ''
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 license = "MIT"
 keywords = []
 authors = [
@@ -19,7 +19,6 @@ authors = [
 classifiers = [
  "Development Status :: 4 - Beta",
  "Programming Language :: Python",
- "Programming Language :: Python :: 3.7",
  "Programming Language :: Python :: 3.8",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
@@ -28,6 +27,7 @@ classifiers = [
  "Programming Language :: Python :: Implementation :: PyPy",
 ]
 dependencies = [
+ "cellpose",
  "confuse",
  "rich",
  "scikit-image",
@@ -55,7 +55,7 @@ cov = "pytest --cov-report=term-missing --cov-config=pyproject.toml --cov=faim_w
 no-cov = "cov --no-cov {args}"
 
 [[tool.hatch.envs.test.matrix]]
-python = ["37", "38", "39", "310", "311"]
+python = ["38", "39", "310", "311"]
 
 [tool.coverage.run]
 branch = true

src/faim_wako_searchfirst/segment.py

@@ -9,8 +9,11 @@
 """
 
 import logging
+from pathlib import Path
+from typing import Union
 
 import numpy as np
+from cellpose import models
 from scipy.ndimage import binary_fill_holes
 from skimage.measure import label, regionprops
 
@@ -26,10 +29,6 @@ def threshold(
  :param img: input image
  :param threshold: global threshold
  :param include_holes: if true, holes will be filled
- :param min_size: minimum object size
- :param max_size: maximum object size
- :param min_eccentricity: minimum eccentricity of object
- :param max_eccentricity: maximum eccentricity of object
  :param logger:
 
  :return: a label image representing the detected objects
@@ -41,3 +40,32 @@ def threshold(
  regions = regionprops(labeled_image)
  logger.info(f"Found {len(regions)} connected components.")
  return labeled_image
+
+
+def cellpose(
+ img,
+ diameter: float,
+ pretrained_model: Union[str, Path] = "cyto2",
+ logger=logging,
+ **kwargs,
+):
+ """Segment a given image by global thresholding.
+
+ :param img: input image
+ :param diameter: expected object diameter
+ :param pretrained_model: name of cellpose model, or path to pretrained model
+ :param logger:
+
+ :return: a label image representing the detected objects
+ """
+ logger.info(f"Load cellpose model: {pretrained_model}")
+ model: models.CellposeModel = models.CellposeModel(
+ pretrained_model=pretrained_model,
+ )
+ mask, _, _ = model.eval(
+ img,
+ channels=[0, 0],
+ diameter=diameter,
+ **kwargs,
+ )
+ return mask

tests/test_cellpose.py

@@ -0,0 +1,36 @@
+# SPDX-FileCopyrightText: 2023 Friedrich Miescher Institute for Biomedical Research (FMI), Basel (Switzerland)
+#
+# SPDX-License-Identifier: MIT
+
+"""Test faim_wako_searchfirst module."""
+import csv
+import shutil
+from pathlib import Path
+
+import pytest
+from faim_wako_searchfirst.main import run
+
+
+@pytest.fixture
+def _data_path(tmp_path):
+ # copy test set into tmp_path, return resulting Path
+ testset_path = Path("tests/resources/TestSet")
+ assert testset_path.exists()
+ return shutil.copytree(testset_path, tmp_path / "TestSet")
+
+
+def test_cellpose(_data_path):
+ """Test run with parameters defined in the sample config_cellpose.yml file."""
+ run(_data_path, configfile="config_cellpose.yml")
+ csv_path = _data_path / "TestSet_D07_T0001F002L01A02Z01C01.csv"
+ assert csv_path.exists()
+ with open(csv_path, "r") as csv_file:
+ reader = csv.reader(csv_file, quoting=csv.QUOTE_NONNUMERIC)
+ entries = list(reader)
+ assert len(entries) == 3, "Incorrect number of objects detected."
+ assert entries[0] == pytest.approx([1, 40.5, 30.5])
+ assert entries[1] == pytest.approx([2, 158.5, 58.5])
+ assert entries[2] == pytest.approx([3, 79.5287, 146.4483])
+
+ segmentation_folder = _data_path.parent / (_data_path.name + "_segmentation")
+ assert sum(1 for _ in segmentation_folder.glob("*")) == 1