diff --git a/README.md b/README.md index f4d8af6..9919ebc 100644 --- a/README.md +++ b/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 ------------- diff --git a/docs/index.markdown b/docs/index.markdown index 5d321c3..644a827 100644 --- a/docs/index.markdown +++ b/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}, +} +``` diff --git a/pyproject.toml b/pyproject.toml index a1d8dc5..cac1007 100644 --- a/pyproject.toml +++ b/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", diff --git a/src/myofinder/__version__.py b/src/myofinder/__version__.py index be46097..f9ac996 100644 --- a/src/myofinder/__version__.py +++ b/src/myofinder/__version__.py @@ -1,3 +1,3 @@ # coding: utf-8 -__version__ = '1.1.0' +__version__ = '1.1.0.post1' diff --git a/src/wix/myofinder.wxs b/src/wix/myofinder.wxs index 87a0d8b..8e12c3c 100644 --- a/src/wix/myofinder.wxs +++ b/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"> + Value="MyoFInDer 1.1.0-post1 Installation [1]" />