Publication

.github/workflows/open_journals_pdf_generation.yml

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+name: Draft PDF
+on:
+    # creates a button
+    workflow_dispatch:
+        inputs:
+            logLevel:
+                description: "Log level"
+                required: true
+                default: "warning"
+                type: choice
+                options:
+                    - info
+                    - warning
+                    - debug
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: publication/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper.pdf

publication/paper.bib

@@ -0,0 +1,144 @@
+@misc{prompt_toolkit,
+author       = {Jonathan Slenders},
+title        = {prompt-toolkit},
+year         = {2023},
+publisher    = {GitHub},
+journal      = {GitHub repository},
+howpublished = {\url{https://github.com/prompt-toolkit/python-prompt-toolkit}}
+}
+
+@article{von2021democratising,
+  title={Democratising deep learning for microscopy with ZeroCostDL4Mic},
+  author={von Chamier, Lucas and Laine, Romain F and Jukkala, Johanna and Spahn, Christoph and Krentzel, Daniel and Nehme, Elias and Lerche, Martina and Hern{\'a}ndez-P{\'e}rez, Sara and Mattila, Pieta K and Karinou, Eleni and others},
+  journal={Nature communications},
+  volume={12},
+  number={1},
+  pages={2276},
+  year={2021},
+  doi={10.1038/s41467-021-22518-0},
+  publisher={Nature Publishing Group UK London}
+}
+
+@article{schindelin2012fiji,
+  title={Fiji: an open-source platform for biological-image analysis},
+  author={Schindelin, Johannes and Arganda-Carreras, Ignacio and Frise, Erwin and Kaynig, Verena and Longair, Mark and Pietzsch, Tobias and Preibisch, Stephan and Rueden, Curtis and Saalfeld, Stephan and Schmid, Benjamin and others},
+  journal={Nature methods},
+  volume={9},
+  number={7},
+  pages={676--682},
+  year={2012},
+  doi={10.1038/nmeth.2019},
+  publisher={Nature Publishing Group US New York}
+}
+
+@misc{saraiva_2025_rxivmaker,
+      title={Rxiv-Maker: an automated template engine for streamlined scientific publications},
+      author={Bruno M. Saraiva and António D. Brito and Guillaume Jaquemet and Ricardo Henriques},
+      year={2025},
+      eprint={2508.00836},
+      archivePrefix={arXiv},
+      primaryClass={cs.DL},
+      doi={10.48550/arXiv.2508.00836},
+      url={https://arxiv.org/abs/2508.00836},
+}
+
+@article{sofroniew2025napari,
+  author       = {Sofroniew, Nicholas and Lambert, Talley and Bokota, Grzegorz and Nunez-Iglesias, Juan and Sobolewski, Piotr and Sweet, Andy and Gaifas, Lorenzo and Evans, Kevin and Burt, Alister and Pop, Draga Doncila and Yamauchi, Kira and Weber Mendonça, Melissa and Liu, Lucy and Buckley, Genevieve and Vierdag, Wouter-Michiel and Monko, Thomas and Royer, Loic and Can Solak, Ahmet and Harrington, Kyle I. S. and Zhao, Ruolan},
+  title        = {napari: a multi-dimensional image viewer for Python (v0.6.2)},
+  journal      = {Zenodo},
+  publisher    = {Zenodo},
+  year         = 2025,
+  doi          = {10.5281/zenodo.15779115},
+  url          = {https://doi.org/10.5281/zenodo.15779115}
+}
+
+@inproceedings{kluyver2016jupyter,
+  author       = {Kluyver, Thomas and Ragan-Kelley, Benjamin and Pérez, Fernando and Granger, Brian and Bussonnier, Matthias and Frederic, Jonathan and Kelley, Kyle and Hamrick, Jessica and Grout, Jason and Corlay, Sylvain and Ivanov, Paul and Avila, Damián and Abdalla, Safia and Willing, Carol},
+  title        = {Jupyter Notebooks – a publishing format for reproducible computational workflows},
+  booktitle    = {Positioning and Power in Academic Publishing: Players},
+  pages        = {87--90},
+  year         = 2016,
+  publisher    = {IOS Press},
+  doi          = {10.3233/978-1-61499-649-1-87},
+  url          = {https://doi.org/10.3233/978-1-61499-649-1-87}
+}
+
+@article{saraiva2025nanopyx,
+  title={Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework},
+  author={Saraiva, Bruno M. and Cunha, In{\^e}s and Brito, Ant{\'o}nio D. and Jacquemet, Guillaume and Henriques, Ricardo},
+  journal={Nature Methods},
+  volume={22},
+  pages={283--286},
+  year={2025},
+  publisher={Nature Publishing Group},
+  doi={10.1038/s41592-024-02562-6},
+  url={https://doi.org/10.1038/s41592-024-02562-6}
+}
+
+@article{mcquin2018cellprofiler,
+  author = {McQuin, Claire and Goodman, Allen and Chernyshev, Vasiliy and Kamentsky, Lee and Cimini, Beth A. and Karhohs, Kyle W. and Doan, Minh and Ding, Liya and Rafelski, Susanne M. and Thirstrup, Derek and et al.},
+  journal = {PLOS Biology},
+  title = {Cellprofiler 3.0: Next-generation image processing for biology},
+  year = {2018},
+  doi={10.1371/journal.pbio.2005970}
+}
+
+@article{demsar2013orange,
+  author  = {Janez Dem\v{s}ar and Toma\v{z} Curk and Ale\v{s} Erjavec and \v{C}rt Gorup and
+  Toma\v{z} Ho\v{c}evar and Mitar Milutinovi\v{c} and Martin Mo\v{z}ina and Matija Polajnar and
+  Marko Toplak and An\v{z}e Stari\v{c} and Miha \v{S}tajdohar and Lan Umek and
+  Lan \v{Z}agar and Jure \v{Z}bontar and Marinka \v{Z}itnik and Bla\v{z} Zupan},
+  title   = {Orange: Data Mining Toolbox in Python},
+  journal = {Journal of Machine Learning Research},
+  year    = {2013},
+  volume  = {14},
+  pages   = {2349-2353},
+  url     = {http://jmlr.org/papers/v14/demsar13a.html}
+}
+
+@article{sandve2013ten,
+  author = {Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
+  journal = {PLoS Computational Biology},
+  number = {10},
+  title = {Ten simple rules for reproducible computational research},
+  volume = {9},
+  year = {2013},
+  doi={10.1371/journal.pcbi.1003285}
+}
+
+@article{DL4MicEverywhere,
+  author = {Hidalgo-Cenalmor, I. and Pylvänäinen, JW and G. Ferreira, M. and Russell, CT and Saguy, A. and Arganda-Carreras, I. and Shechtman, Y. and AI4Life Horizon Europe Program Consortium and Jacquemet, G. and Henriques, R. and Gómez-de-Mariscal, E.},
+  journal = {nature Methods},
+  number = {},
+  title = {DL4MicEverywhere: deep learning for microscopy made flexible, shareable and reproducible.},
+  volume = {21},
+  year = {2024},
+  doi={10.1038/s41592-024-02295-6}
+}
+
+@article{imagej,
+  author = {Schneider, C. and Rasband, W. and Eliceiri, K.},
+  journal = {Nature Methods},
+  number = {},
+  title = {NIH Image to ImageJ: 25 years of image analysis.},
+  volume = {9},
+  year = {2012},
+  doi={10.1038/nmeth.2089}
+}
+
+@misc{colab,
+  author       = {Google},
+  title        = {Google Colaboratory},
+  year         = 2024,
+  url          = {https://colab.research.google.com/}
+}
+
+@article{colabfold,
+  author = {},
+  journal = {Nature Methods},
+  number = {19},
+  title = {ColabFold: making protein folding accessible to all},
+  volume = {},
+  year = {2022},
+  doi = {10.1038/s41592-022-01488-1}
+}