Adds Zenodo DOI and authors

README.md

@@ -1,3 +1,7 @@
+Zenodo DOI: [![DOI](https://zenodo.org/badge/417468733.svg)](https://zenodo.org/doi/10.5281/zenodo.10829243)
+
+
+
 # QuPath Cellpose/Omnipose extension
 
 This repo adds some support to use 2D Cellpose within QuPath through a Python virtual environment.
@@ -12,6 +16,41 @@ they can play nice.
 > Versions above v0.6.0 of this extension **will only work on QuPath 0.4.0 or later**. Please update QuPath to the latest version. 
 > In case you are stuck with QuPath v0.3.2, [the last release to work is v0.5.1](https://github.com/BIOP/qupath-extension-cellpose/releases/tag/v0.5.1)
 
+
+# Citing
+
+Please cite this extension by linking it to this GitHub or to the release you used, and feel free to give us a star ⭐️
+
+As this code is neither novel nor entirely original, there is no linked publication, but you can use the following Zenodo entry:
+
+[![DOI](https://zenodo.org/badge/417468733.svg)](https://zenodo.org/doi/10.5281/zenodo.10829243)
+
+## Code authorship
+**Author**: Olivier Burri (1)
+
+**Contributors**: Nicolas Chiaruttini (1), Romain Guiet (1)
+
+This code heavily makes use of functions created by Pete Bankhead and the QuPath team for their [StarDist Extension](https://github.com/qupath/qupath-extension-stardist)
+
+**Affiliations**
+
+(1) EPFL BioImaging and Optics Platform (BIOP)
+
+### If you use this extension, you should cite the following publications
+
+Stringer, C., Wang, T., Michaelos, M. et al **Cellpose: a generalist algorithm for cellular segmentation**. Nat Methods 18, 100–106 (2021). https://doi.org/10.1038/s41592-020-01018-x
+
+Pachitariu, M., Stringer, C. **Cellpose 2.0: how to train your own model**. Nat Methods 19, 1634–1641 (2022). https://doi.org/10.1038/s41592-022-01663-4
+
+Cutler, K.J., Stringer, C., Lo, T.W. et al. **Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation**. Nat Methods 19, 1438–1448 (2022). https://doi.org/10.1038/s41592-022-01639-4
+
+Bankhead, P. et al. **QuPath: Open source software for digital pathology image analysis**. Scientific Reports (2017). https://doi.org/10.1038/s41598-017-17204-5
+
+
+
+
+
+
 # Installation
 
 ## Step 1: Install Cellpose and/or Omnipose
@@ -246,22 +285,6 @@ In order to make the extension more flexible and less dependent on the builder,
 For this to work, some elements that were "hard coded" on the builder have been removed, so you will get some errors. For example: `excludeEdges()` and `clusterDBSCAN()` no longer exist. 
 You can use `addParameter("exclude_on_edges")`, and `addParameter("cluster")` instead.
 
-# Citing
-
-Please cite this extension by linking it to this GitHub or to the release you used, and feel free to give us a star ⭐️
-
-If you use this extension, you should cite the following publications
-
-Stringer, C., Wang, T., Michaelos, M. et al **Cellpose: a generalist algorithm for cellular segmentation**. Nat Methods 18, 100–106 (2021). https://doi.org/10.1038/s41592-020-01018-x
-
-Pachitariu, M., Stringer, C. **Cellpose 2.0: how to train your own model**. Nat Methods 19, 1634–1641 (2022). https://doi.org/10.1038/s41592-022-01663-4
-
-Cutler, K.J., Stringer, C., Lo, T.W. et al. **Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation**. Nat Methods 19, 1438–1448 (2022). https://doi.org/10.1038/s41592-022-01639-4
-
-Bankhead, P. et al. **QuPath: Open source software for digital pathology image analysis**. Scientific Reports (2017).
-https://doi.org/10.1038/s41598-017-17204-5
-
-
 # Building
 
 You can build the QuPath Cellpose extension from source with