Merge pull request #12 from Image-Analysis-Hub/epidev

Epidev

Author: gletort

README.md

@@ -1,12 +1,14 @@
 # EpiCure
 
-[![License BSD-3](https://img.shields.io/pypi/l/epicure.svg?color=green)](https://github.com/gletort/Epicure/-/blob/main/LICENSE)
+[![License BSD-3](https://img.shields.io/pypi/l/epicure.svg?color=green)](https://github.com/Image-Analysis-Hub/Epicure/blob/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/epicure.svg?color=green)](https://pypi.org/project/epicure)
 [![Python Version](https://img.shields.io/pypi/pyversions/epicure.svg?color=green)](https://python.org)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/epicure)](https://napari-hub.org/plugins/epicure)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13952184.svg)](https://doi.org/10.5281/zenodo.13952184)
 
-![EpiCure logo](https://github.com/gletort/Epicure/blob/main/docs/imgs/epicure_logo.png "EpiCure logo")
+![EpiCure logo](https://github.com/Image-Analysis-Hub/Epicure/blob/main/docs/imgs/epicure_logo.png "EpiCure logo")
+![CNRS logo](https://github.com/Image-Analysis-Hub/Epicure/blob/main/docs/imgs/logo_cnrs.png "CNRS logo")
+![DSCB logo](https://github.com/Image-Analysis-Hub/Epicure/blob/main/docs/imgs/logo_DSCB.png "DSCB logo")
 
 **Napari plugin to ease manual correction of epithelia segmentation in movies.**
 
@@ -19,9 +21,9 @@ Several features are proposed to ease the manual correction of the segmented mov
 EpiCure detect segmentation errors by taking advantage of temporal information. 
 When a correction is done at a given frame, EpiCure relink the track to adjust for the changes.
 
- > **See the full [documentation here](https://gletort.github.io/Epicure/)**
+ > **See the full [documentation here](https://image-analysis-hub.github.io/Epicure/)**
 
-![EpiCure interface](https://github.com/gletort/Epicure/blob/main/docs/imgs/EpiGen.png "EpiCure interface")
+![EpiCure interface](https://github.com/Image-Analysis-Hub/Epicure/blob/main/docs/imgs/EpiGen.png "EpiCure interface")
 
 ## Installation
 
@@ -46,20 +48,26 @@ Tracking options are proposed in EpiCure:
 * Laptrack overlaps
 
 ## Usage
-Refer to the [documentation](https://gletort.github.io/Epicure/) for documentation of the different steps possible in the pipeline.
+Refer to the [documentation](https://image-analysis-hub.github.io/Epicure/) for documentation of the different steps possible in the pipeline.
 
 ## References
 
 If you use EpiCure, thank you for citing our work: 
 
 EpiCure is not published yet, you can cite it using Zenodo for now: https://doi.org/10.5281/zenodo.13952184
 
-
-## Issues
-If you encounter a code related issue using EpiCure, please [file an issue](https://github.com/gletort/epicure/issues) in this repository.
+## Contributing and Feedback
+EpiCure is mainly developed in CNRS UMR3738, in the [Developmental and Stem Cell Biology Department](https://research.pasteur.fr/en/department/developmental-stem-cell-biology/) of Institut Pasteur.
 If you have a question on using EpiCure or ask to add a feature, either file an issue or write in the [imagesc forum](https://forum.image.sc/).
 
+Any contribution is most welcome. 
+Do not hesitate to contact us beforehand through [filing an issue](https://github.com/Image-Analysis-Hub/epicure/issues/) (choose "Other questions/comments" type).
+To suggest the addition of a new feature, you can also contact us by filing an issue choosing the "Feature request" option.
+
+If you encounter a code related issue using EpiCure, please [file an issue](https://github.com/Image-Analysis-Hub/epicure/issues) in this repository.
+
+
 [napari]: https://github.com/napari/napari
-[file an issue]: https://github.com/gletort/epicure/issues
+[file an issue]: https://github.com/Image-Analysis-Hub/epicure/issues
 [pip]: https://pypi.org/project/pip/
 [PyPI]: https://pypi.org/

docs/imgs/logo_cnrs.png

@@ -54,12 +54,12 @@ def show_debug(message):
 
 def show_documentation():
     import webbrowser
-    webbrowser.open_new_tab("https://gletort.github.io/Epicure/")
+    webbrowser.open_new_tab("https://image-analysis-hub.github.io/Epicure/")
     return
 
 def show_documentation_page(page):
     import webbrowser
-    webbrowser.open_new_tab("https://gletort.github.io/Epicure/"+page)
+    webbrowser.open_new_tab("https://image-analysis-hub.github.io/Epicure/"+page)
     return
 
 def show_progress( viewer, show ):

docs/imgs/logo_dscb.png

@@ -17,5 +17,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.dev135+g785d2b9.d20260216'
-__version_tuple__ = version_tuple = (0, 1, 'dev135', 'g785d2b9.d20260216')
+__version__ = version = '0.1.dev137+ga8d5a62.d20260216'
+__version_tuple__ = version_tuple = (0, 1, 'dev137', 'ga8d5a62.d20260216')

src/epicure/Utils.py

@@ -653,6 +653,7 @@ def save_epicures(self, imtype="float32"):
         ut.writeTif(self.seg, outname, self.epi_metadata["ScaleXY"], imtype, what="Segmentation")
         epiname = os.path.join(self.outdir, self.imgname + "_epidata.pkl")
         outfile = open(epiname, "wb")
+        self.epi_metadata["MainChannel"] = self.main_channel 
         epidata = {}
         epidata["EpiMetaData"] = self.epi_metadata
         if self.groups is not None:

src/epicure/_version.py

@@ -97,6 +97,8 @@ def load_movie_from_layers(movie, movie_path, segmented):
         get_files.allow_gaps.value = bool(Epic.epi_metadata["Allow gaps"])
         get_files.verbose_level.value = int(Epic.epi_metadata["Verbose"])
         get_files.call_button.enabled = True
+        if "MainChannel" in Epic.epi_metadata:
+            get_files.junction_chanel.value = int(Epic.epi_metadata["MainChannel"])
 
     def show_metatdata(show=True):
         """ Show or update the metadata parameters """
@@ -131,6 +133,8 @@ def load_movie():
         get_files.segment_with_epyseg.visible = True
         get_files.allow_gaps.value = bool(Epic.epi_metadata["Allow gaps"])
         get_files.verbose_level.value = int(Epic.epi_metadata["Verbose"])
+        if "MainChannel" in Epic.epi_metadata:
+            get_files.junction_chanel.value = int(Epic.epi_metadata["MainChannel"])
         get_files.call_button.enabled = True
         ut.show_duration(start_time, header="Movie loaded in ")