Image data science with Python and Napari

Image data science with Python and Napari#

A first Latin America workshop #LIBREhub @napari #LABI - Latin America Bioimaging #MexicoBioimaging

This Jupyter book contains training resources for scientists who want to dive into image processing with Python and Napari. It specifically aims for scientists and students working with microscopy images in the life sciences. We presume the attendees have some basic python programming and image analysis knowledge. To get everyone on the same level, we start with Python programming basics. We will process images using numpy, scipy, scikit-image, SimpleITK and clEsperanto. We will explore Napari for interactive image data analysis and the Napari-Assistant for generating Jupyter Notebooks from interactively designed image processing workflows.

Note: Before the course starts, all partcipants are required to have Napari and Jupyter installed, please see the course preparation page - and make use of the napari chatroom for troubleshooting if you face installation issues. The session on Python environments is further more in the inverted classroom format, so we kindly ask that you familiarise yourself with the dedicated teaching material on environments before the session in order to simply use the given time for questions.

Timetable#

All following times are in Chilean (Santiago) time (currently GMT-4). Look up your related time here, so you don’t miss anything.

Day 1 - Monday the 7th of August 2023#

Time (Chile)	Activities / Topics	Presenters	Support
08.00 – 09.00	Motivating talk - Napari bioimage analysis	Juan Nunez-Iglesias, video	–
09.00 – 09.55	Welcome and ice-break Session	Tobias Wenzel (host) slides	Pierre Padilla Huamantico
10.10 – 12.00	Environments Q & A installation and set-up	Peter Sobolewski	Marcelo Zoccoler, Tobias Wenzel
12:00 - 13:00	Lunch Break
13.00 – 14.55	Introduction to the napari assistant and exporting workflows to jupyter notebooks	Robert Haase slides pptx, PDF, video	Marcelo Zoccoler
15.10 – 16.30	• Pitfalls when working with Jupyter notebooks • Basic types in python • Lists and tuples • Cropping lists • Cropping images	Marcelo Zoccoler slides1, video1, slides2, video2	Adan Guerrero Cardenas, Pierre Padilla Huamantico, Guillermo Sahonero Alvarez, Jorge Gonzalez
16.30 – 17.30	• Masking numpy arrays • Dictionaries • Conditions • Loops • Functions	Melissa Weber Mendonça, video	Adan Guerrero Cardenas, Pierre Padilla Huamantico, Guillermo Sahonero Alvarez, Jorge Gonzalez

Day 2 - Wednesday the 9th of August 2023#

Time (Chile)	Activities / Topics	Presenters	Support
10:30 - 11:00	Questions from the last day?	Marcelo Zoccoler	Tobias Wenzel, Adan Guerrero Cardenas, Pierre Padilla Huamantico, Guillermo Sahonero Alvarez, Jorge Gonzalez
11.00 – 12.00	Python advanced folder management with loops • Open proprietary file formats	Marcelo Zoccoler slides	Adan Guerrero Cardenas, Pierre Padilla Huamantico, Guillermo Sahonero Alvarez, Jorge Gonzalez
12.00 – 14.00	Tips for open source image analysis	Rocco D’Antuono slides	–
14:00 - 16:00	Lunch Break
16.00 – 19.00	Image analysis under the hood with python and napari: • Understanding filters (smoothing, edge detection) • Hands on segmentation, thresholding, labelling and measurement	Juan Nunez-Iglesias	Adan Guerrero Cardenas, Daniel Althviz Moré

If you run the exercises in your own time and questions arise, please ask on https://forum.image.sc/.

Day 3 - Friday the 11th of August 2023 open to all here on Zoom #

On the third and last day, there are showcase seminars of key napari plugins as well as emerging trends to controll your bioimaging hardware with python libraries.

Time	Activities / Topics	Presenters
07.55 – 08.00	Welcome!	Tobias Wenzel (host)
08.00 – 08.20	Napari Animation	Juan Nunez-Iglesias, video
08:20-8:50	Affinder	Juan Nunez-Iglesias, video
08:50 – 9:30	Napari Clusters Plotter (Unsupervised machine learning)	Marcelo Zoccoler, video
09:30 - 10:00	Break
10.10 – 11.00	Napari Zelda (3D segmentation)	Rocco D’Antuono, video
11.00 – 12.00	Napari Superres (Superresolution)	Julián Mejía, video
12:00 - 12:40	Napari real time processing	Lucien Hinderling, video
12:40 - 14:00	Lunch Break
14:00 - 15:00	Python libraries for microscope control	Talley Lambert

How to use this material#

For following the course, we recommend downloading the repository from which this Jupyter book is made. All Jupyter Notebooks are executable so that attendees can reproduce all demos and exercises.

Assuming you downloaded the repository to your Desktop, you can open the Jupyter book by opening a terminal and typing:

cd Desktop/napari-LatAm-workshop-2023

micromamba activate napari-latam

jupyter lab

If you do not yet have conda or devbio-napari-env installed, first follow the “Course preparation” installation instructions on the next page.

Using Jupyter lab, you can navigate to the course lessons in the docs folder.

… and execute the code and experiment with it.

Feedback and support#

If you have any questions, please create a github issue. Alternatively, open a thread on image.sc.

Acknowledgements#

This course was held virtually at the Institute for Biological and Medical Engineering, Universidad Católica de Chile in August 2023 as part of the LIBRE hub project. We would like to thank all online contributors and speakers for their support and the Chan Zuckerberg Initiative for financial support through the LIBRE hub project. We would like to thank all the people who shared teaching materials we are reusing here, in particular from an EPFL copurse last year and individual contributors including 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.