cellfinder 1.3.0rc2__tar.gz → 1.3.2__tar.gz

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/.github/workflows/test_and_deploy.yml

@@ -44,15 +44,15 @@ jobs:
       matrix:
         # Run all supported Python versions on linux
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         # Include one windows and two macOS (intel based and arm based) runs
         include:
           - os: macos-13
-            python-version: "3.11"
+            python-version: "3.12"
           - os: macos-latest
-            python-version: "3.11"
+            python-version: "3.12"
           - os: windows-latest
-            python-version: "3.11"
+            python-version: "3.12"
 
     steps:
       - name: Cache brainglobe directory
@@ -98,7 +98,7 @@ jobs:
       # Run test suite with numba disabled
       - uses: neuroinformatics-unit/actions/test@v2
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           codecov-flags: "numba"
 
@@ -125,10 +125,10 @@ jobs:
         with:
           repository: 'brainglobe/brainglobe-workflows'
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v3
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install test dependencies
         run: |

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/.github/workflows/test_include_guard.yaml

@@ -22,7 +22,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install cellfinder via pip
         run: python -m pip install -e "."

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc2
+Version: 1.3.2
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -16,11 +16,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: brainglobe-utils>=0.5.0
@@ -29,7 +29,7 @@ Requires-Dist: dask[array]
 Requires-Dist: fancylog>=0.0.7
 Requires-Dist: natsort
 Requires-Dist: numba
-Requires-Dist: numpy
+Requires-Dist: numpy<2
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: keras>=3.0.0
@@ -101,8 +101,14 @@ pip install cellfinder>=1.0.0
 Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.
 See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.
 
-## Contributing
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
 
-If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues).
+## Citation
+If you find this package useful, and use it in your research, please cite the following paper:
+> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
+[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
 
-If you are interested in contributing to cellfinder (thank you!) - please head over to our [developer documentation](https://brainglobe.info/community/developers/index.html).
+**If you use this, or any other tools in the brainglobe suite, please
+ [let us know](https://brainglobe.info/contact.html), and
+ we'd be happy to promote your paper/talk etc.**

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/README.md

@@ -44,8 +44,14 @@ pip install cellfinder>=1.0.0
 Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.
 See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.
 
-## Contributing
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
 
-If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues).
+## Citation
+If you find this package useful, and use it in your research, please cite the following paper:
+> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
+[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
 
-If you are interested in contributing to cellfinder (thank you!) - please head over to our [developer documentation](https://brainglobe.info/community/developers/index.html).
+**If you use this, or any other tools in the brainglobe suite, please
+ [let us know](https://brainglobe.info/contact.html), and
+ we'd be happy to promote your paper/talk etc.**

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/cellfinder/core/detect/filters/volume/structure_splitting.py

@@ -74,6 +74,7 @@ def ball_filter_imgs(
     good_tiles_mask = np.ones((1, 1, volume.shape[2]), dtype=np.bool_)
 
     plane_width, plane_height = volume.shape[:2]
+    current_z = ball_z_size // 2
 
     bf = BallFilter(
         plane_width,
@@ -86,9 +87,7 @@ def ball_filter_imgs(
         threshold_value=threshold_value,
         soma_centre_value=soma_centre_value,
     )
-    cell_detector = CellDetector(
-        plane_width, plane_height, start_z=ball_z_size // 2
-    )
+    cell_detector = CellDetector(plane_width, plane_height, start_z=current_z)
 
     # FIXME: hard coded type
     ball_filtered_volume = np.zeros(volume.shape, dtype=np.uint32)
@@ -98,7 +97,11 @@ def ball_filter_imgs(
         if bf.ready:
             bf.walk()
             middle_plane = bf.get_middle_plane()
-            ball_filtered_volume[:, :, z] = middle_plane[:]
+
+            # first valid middle plane is the current_z, not z
+            ball_filtered_volume[:, :, current_z] = middle_plane[:]
+            current_z += 1
+
             # DEBUG: TEST: transpose
             previous_plane = cell_detector.process(
                 middle_plane.copy(), previous_plane
@@ -134,7 +137,10 @@ def iterative_ball_filter(
         vol, cell_centres = ball_filter_imgs(
             vol, threshold_value, soma_centre_value
         )
-        vol -= 1
+
+        # vol is unsigned, so can't let zeros underflow to max value
+        vol[:, :, :] = np.where(vol != 0, vol - 1, 0)
+
         n_structures = len(cell_centres)
         ns.append(n_structures)
         centres.append(cell_centres)

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/cellfinder/napari/curation.py

@@ -113,7 +113,7 @@ class CurationWidget(QWidget):
         layer_names = [
             layer.name
             for layer in self.viewer.layers
-            if type(layer) == layer_type
+            if isinstance(layer, layer_type)
         ]
 
         if layer_names:
@@ -329,7 +329,7 @@ class CurationWidget(QWidget):
 
         if len(self.viewer.layers.selection) == 1:
             layer = list(self.viewer.layers.selection)[0]
-            if type(layer) == napari.layers.Points:
+            if isinstance(layer, napari.layers.Points):
                 if len(layer.data) > 0:
                     if point_type == "cell":
                         destination_layer = self.training_data_cell_layer

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/cellfinder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc2
+Version: 1.3.2
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -16,11 +16,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: brainglobe-utils>=0.5.0
@@ -29,7 +29,7 @@ Requires-Dist: dask[array]
 Requires-Dist: fancylog>=0.0.7
 Requires-Dist: natsort
 Requires-Dist: numba
-Requires-Dist: numpy
+Requires-Dist: numpy<2
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: keras>=3.0.0
@@ -101,8 +101,14 @@ pip install cellfinder>=1.0.0
 Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.
 See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.
 
-## Contributing
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
 
-If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues).
+## Citation
+If you find this package useful, and use it in your research, please cite the following paper:
+> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
+[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
 
-If you are interested in contributing to cellfinder (thank you!) - please head over to our [developer documentation](https://brainglobe.info/community/developers/index.html).
+**If you use this, or any other tools in the brainglobe suite, please
+ [let us know](https://brainglobe.info/contact.html), and
+ we'd be happy to promote your paper/talk etc.**

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/cellfinder.egg-info/requires.txt

@@ -4,7 +4,7 @@ dask[array]
 fancylog>=0.0.7
 natsort
 numba
-numpy
+numpy<2
 scikit-image
 scikit-learn
 keras>=3.0.0

{cellfinder-1.3.0rc2 → cellfinder-1.3.2}/pyproject.toml

@@ -14,12 +14,12 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Image Recognition",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "brainglobe-utils>=0.5.0",
     "brainglobe-napari-io>=0.3.4",
@@ -27,7 +27,7 @@ dependencies = [
     "fancylog>=0.0.7",
     "natsort",
     "numba",
-    "numpy",
+    "numpy<2",
     "scikit-image",
     "scikit-learn",
     "keras>=3.0.0",
@@ -79,7 +79,7 @@ requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = 'setuptools.build_meta'
 
 [tool.black]
-target-version = ['py39', 'py310','py311']
+target-version = ['py310','py311', 'py312']
 skip-string-normalization = false
 line-length = 79
 
@@ -111,14 +111,14 @@ markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
 legacy_tox_ini = """
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{39,310,311}
+envlist = py{310,311,312}
 isolated_build = true
 
 [gh-actions]
 python =
-    3.9: py39
     3.10: py310
     3.11: py311
+    3.12: py312
 
 [testenv]
 commands = python -m pytest -v --color=yes --cov=cellfinder --cov-report=xml