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napari-latam-workshop-2023's Introduction

napari LatAm workshop

CC BY 4.0 Open Source Love

This work is licensed openly by Marcelo Leomil Zoccoler, Tobias Wenzel, Juan Nunez-Iglesias, Rocco D'Antuono, Melissa Weber Mendonça, Talley Lambert, Julián Mejía, Adan O. Guerrero Cardenas, and Robert Haase under a Creative Commons Attribution 4.0 International License unless mentioned otherwise. @LIBREhub, @Latin America Bioimaging, @Napari 2023

This repository hosts notebooks, information and data for the "Image data science with Python and Napari" remote Latin America workshop in August 2023.

This is the link to the online jupyter book of the course: https://librehub.github.io/napari-LatAm-workshop-2023/ rendered from this repository.

It is maintained using Jupyter lab and build using Jupyter book.

Acknowledgements

This course is held virtually for Latin American participants in August 2023 and with Spanish and Portuguese language support. The workshop is organised by the LIBRE hub project and is the result of a collaboration and support by a number of individuals and CZI funded initiatives driving access to bioimaging research capabilities, including individuals from Napari, Latin America Bioimaging, Mexico Bioimaging,and available online material. We would like to thank the Chan Zuckerberg Initiative for financial support through the LIBRE hub project and the other participating initiatives.

This work is forked and modified from a EPFL course developed and licensed by Marcelo Leomil Zoccoler, Johannes Richard Müller, Till Korten and Robert Haase, PoL Dresden under a Creative Commons Attribution 4.0 International License.

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napari-latam-workshop-2023's Issues

Environment notes for next time?

  1. A lot of folks had anaconda already, which led to some issues with running (micro)mamba I think due to CONDA env vars and prefixes. Should add a section on this specifically—for better or worse, anaconda has been very well popularized. I think it should be possible to run micromamba in parallel, but definitely need to investigate. One option is to let those folks keep using their existing anaconda with conda-forge and lib mamba solver referencing to:
  1. The single env for the whole workshop is simple, but it's gigantic, with >450 packages—I dare say it's anaconda-esque! It takes a while to solve, download, and install—even on a pretty new and fast computer with top-notch internet. It might be better—and also illustrate best practice—to break it up into dedicated envs for (some of) the sub tutorials? With caching and stuff it should be more manageable even if one of the tutorials does need everything.

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