Releases: christophe-pouzat/ENP2017
Course material for C Pouzat's ENP 2017 and 2018 lectures
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.