Course material for the ENP June 20 2017 and May 22 2018 lectures: "Fluorescence Imaging Analysis: The Case of Calcium Transients."

The slides of the lecture are in files Pouzat_ENP2017.pdf and Pouzat_ENP2018.pdf (only cosmetic changes and spelling mistakes corrections compared to 2017). The handout, nicer for printing, with some additional stuff is in files Pouzat_ENP2017_handout.pdf and Pouzat_ENP2018_handout.pdf. All the analysis is done with C together with the GSL library (the Gnu Scientific Library), while figures are done with gnuplot. The C code together with the full details of the whole analysis can be found in file ENP2017_technical_notes.html. The C source files are in directory code. All figures except one are created as part of the analysis--the gnuplot code generating the figures is therefore found in ENP2017_technical_notes.html--.

Each of the files mentioned above are generated from their org source file (files with the same prefix terminating with the .org suffix). The C code is presented following Don Knuth's literate programming paradigm implemented in org (see the paper of Eric Schulte, Dan Davison, Thomas Dye, Carsten Dominik A Multi-Language Computing Environment for Literate Programming and Reproducible Research, 2012, to understand what that means and how that works).

The only actual code contained in Pouzat_ENP2017.org, Pouzat_ENP2017_handout.pdf, Pouzat_ENP2018.org and Pouzat_ENP2018_handout.pdf shows how to automatically download a pdf file from the web, open it at a specific page and extract a specific figure (more precisely a specific part of the page)--all that exclusively from the command line--. This is used to get the only figure of the lecture that is not a result of the analysis.

The same analysis performed with Python can be found at: https://github.com/christophe-pouzat/ENP2015, while the R implementation is available at: http:org/Pouzat-ENP-2013.org.