Release version 1.1.0.post1

README.md

@@ -5,6 +5,20 @@ The MyoFInDer Python package aims to provide an open-source graphical interface
 for automatic calculation of the fusion index in muscle cell cultures, based on 
 fluorescence microscopy images.
 
+> [!IMPORTANT]
+> MyoFInDer is currently in maintenance-only development phase. This means that
+> reported bugs will be fixed, minor changes will be brought to support new
+> Python versions if possible, but no major improvements or updates should be 
+> expected. User requests for new features could still be addressed, depending
+> on how large they are.
+
+> [!WARNING]
+> MyoFInDer version 1.1.0 now uses [CellPose](https://www.cellpose.org/) for 
+> nuclei segmentation instead of [DeepCell](https://www.deepcell.org/). This is
+> a major breaking change. Differences are to be expected in the results 
+> obtained with version 1.1.0 and earlier ones, even with similar processing
+> parameters.
+
 Presentation
 ------------
 
@@ -62,6 +76,17 @@ A more detailed description of the installation procedure can be found in the
 [installation section](https://tissueengineeringlab.github.io/MyoFInDer/installation.html)
 of the documentation.
 
+Citing MyoFInDer
+----------------
+
+If MyoFInDer has been of help in your research, please reference it in your 
+academic publications by citing the following article:
+
+- Weisrock A., Wüst R., Olenic M. et al., *MyoFInDer: An AI-Based Tool for 
+Myotube Fusion Index Determination*, Tissue Eng. Part A (30), 19-20, 2024, 
+DOI: 10.1089/ten.TEA.2024.0049. 
+([link to Weisrock et al.](https://www.liebertpub.com/doi/10.1089/ten.tea.2024.0049))
+
 Documentation
 -------------
 

docs/index.markdown

@@ -21,6 +21,20 @@ On this documentation website, you can find information about the :
 - [Usage](usage.markdown)
 - [Troubleshooting](troubleshooting.markdown)
 
+> [!IMPORTANT]
+> MyoFInDer is currently in maintenance-only development phase. This means that
+> reported bugs will be fixed, minor changes will be brought to support new
+> Python versions if possible, but no major improvements or updates should be 
+> expected. User requests for new features could still be addressed, depending
+> on how large they are.
+
+> [!WARNING]
+> MyoFInDer version 1.1.0 now uses [CellPose](https://www.cellpose.org/) for 
+> nuclei segmentation instead of [DeepCell](https://www.deepcell.org/). This is
+> a major breaking change. Differences are to be expected in the results 
+> obtained with version 1.1.0 and earlier ones, even with similar processing
+> parameters.
+
 # About
 
 This module is **free and open-source**, hosted and distributed on 
@@ -30,3 +44,28 @@ GPL-3.0 license. It was developed at the
 the [KU Leuven KULAK](https://kulak.kuleuven.be/) university. **Contributions,
 bug reports or simple questions** are welcome in the dedicated sections of the
 GitHub page.
+
+# Citing
+
+If MyoFInDer has been of help in your research, please reference it in your 
+academic publications by citing the following article:
+
+- Weisrock A., Wüst R., Olenic M. et al., *MyoFInDer: An AI-Based Tool for 
+Myotube Fusion Index Determination*, Tissue Eng. Part A (30), 19-20, 2024, 
+DOI: 10.1089/ten.TEA.2024.0049. 
+([link to Weisrock et al.](https://www.liebertpub.com/doi/10.1089/ten.tea.2024.0049))
+
+Here is the BibTex code for referencing the article:
+
+```bibtex
+@article{Weisrock2024,
+         author = {Weisrock, Antoine and W\"{u}st, Rebecca and Olenic, Maria and Lecomte-Grosbras, Pauline and Thorrez, Lieven},
+         title = {MyoFInDer: An AI-Based Tool for Myotube Fusion Index Determination},
+         journal = {Tissue Engineering Part A},
+         volume = {30},
+         number = {19-20},
+         pages = {652-661},
+         year = {2024},
+         doi = {10.1089/ten.tea.2024.0049},
+}
+```

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "myofinder"
 dynamic = ["readme", "dependencies"]
-version = "1.1.0"
+version = "1.1.0.post1"
 description = "Automatic calculation of the fusion index by AI segmentation"
 license = "GPL-3.0-or-later"
 license-files = ["LICENSE"]
@@ -14,7 +14,7 @@ requires-python = ">=3.9"
 authors = [{name = "Tissue Engineering Lab", email = "antoine.weisrock@kuleuven.be"}]
 maintainers = [{name = "Antoine Weisrock", email = "antoine.weisrock@gmail.com"}]
 classifiers = [
-    "Development Status :: 4 - Beta",
+    "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
     "Natural Language :: English",
     "Operating System :: OS Independent",

src/myofinder/__version__.py

@@ -1,3 +1,3 @@
 # coding: utf-8
 
-__version__ = '1.1.0'
+__version__ = '1.1.0.post1'

src/wix/myofinder.wxs

@@ -15,7 +15,7 @@
         Scope="perUser"
         ShortNames="no"
         UpgradeCode="D3F780C0-8A53-44E1-81EB-570D9AE61393"
-        Version="1.1.0">
+        Version="1.1.0-post1">
 
         <!-- More information about the installer -->
         <SummaryInformation
@@ -35,7 +35,7 @@
         <!-- Default fields -->
         <Property
             Id="DiskPrompt"
-            Value="MyoFInDer 1.1.0 Installation [1]" />
+            Value="MyoFInDer 1.1.0-post1 Installation [1]" />
 
         <!-- List of the features to install -->
         <Feature