cellfinder 1.3.0rc2__py3-none-any.whl → 1.3.1__py3-none-any.whl

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.dist-info → cellfinder-1.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc2
+Version: 1.3.1
 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
@@ -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.dist-info → cellfinder-1.3.1.dist-info}/RECORD

@@ -22,7 +22,7 @@ cellfinder/core/detect/filters/plane/tile_walker.py,sha256=lhKrq-MB35bR0_JYgj7WM
 cellfinder/core/detect/filters/volume/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/core/detect/filters/volume/ball_filter.py,sha256=ZEg8FNty-VD5N9j4FLZ18G-BuSvxjHs2-QTblwKcZgw,13894
 cellfinder/core/detect/filters/volume/structure_detection.py,sha256=mTHi0_A9FCK39I6fZm2dfMpDxIkfaidOIf6eCjTw-70,11307
-cellfinder/core/detect/filters/volume/structure_splitting.py,sha256=XzTYguVT8VdTu2h4-Jdt5Yyeu8VBYmdRo5jmwwLwuck,7660
+cellfinder/core/detect/filters/volume/structure_splitting.py,sha256=DnYcCkcdEaubzaWxbM7Ee8icyHq3dN8CcvZj_i0QvGM,7880
 cellfinder/core/detect/filters/volume/volume_filter.py,sha256=BJ8bStlNvMWsGlBekeqXpS8d9YKoLe3ifMfrEPpva2Q,7035
 cellfinder/core/download/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/core/download/cli.py,sha256=X9L9ZIkWqs58hX8G8q_0AKN4gk8BhydGxI9nLpdHQQE,1764
@@ -51,9 +51,9 @@ cellfinder/napari/detect/thread_worker.py,sha256=PWM3OE-FpK-dpdhaE_Gi-2lD3u8sL-S
 cellfinder/napari/train/__init__.py,sha256=xo4CK-DvSecInGEc2ohcTgQYlH3iylFnGvKTCoq2WkI,35
 cellfinder/napari/train/train.py,sha256=zJY7zKcLqDTDtD76thmbwViEU4tTFCmXZze-zHsTpoo,5941
 cellfinder/napari/train/train_containers.py,sha256=1wZ_GPe7B5XsLYs5XIx4m8GMw5KeVhg6SchhPtXu4V8,4386
-cellfinder-1.3.0rc2.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
-cellfinder-1.3.0rc2.dist-info/METADATA,sha256=DlFtBgJoeh7SHPbvxuQ7hn-jyLLylKYjCy6rUHBMdLA,6531
-cellfinder-1.3.0rc2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-cellfinder-1.3.0rc2.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
-cellfinder-1.3.0rc2.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
-cellfinder-1.3.0rc2.dist-info/RECORD,,
+cellfinder-1.3.1.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
+cellfinder-1.3.1.dist-info/METADATA,sha256=tdKnKSv42LLsTm89qJdCx0EuRLSDj8XN1gzl8XuB8cM,7097
+cellfinder-1.3.1.dist-info/WHEEL,sha256=-oYQCr74JF3a37z2nRlQays_SX2MqOANoqVjBBAP2yE,91
+cellfinder-1.3.1.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
+cellfinder-1.3.1.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
+cellfinder-1.3.1.dist-info/RECORD,,

{cellfinder-1.3.0rc2.dist-info → cellfinder-1.3.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (71.0.3)
 Root-Is-Purelib: true
 Tag: py3-none-any