Last updated: 1/31/25
Code and small-size data files for generating all results and figures presented in the manuscript, "Searching for the cellular underpinnings of the selective vulnerability to tauopathic insults in Alzheimer's disease" (currently in press at Commuications Biology).
All code herein is original, with the exception of the violin.m package developed by Holger Hoffman (URL, included).
Code is compatible with MATLAB v.2023b, but should work with previous versions of MATLAB as well.
Manuscript Authors: Justin Torok ([email protected]), Pedro D. Maia, Chaitali Anand, Ashish Raj ([email protected]) Code Owner: Justin Torok Additional Code Maintainers: Nuutti Barron ([email protected]) and Robin Sandell ([email protected])
Larger dependencies can be downloaded from Dryad (link forthcoming; DOI: 10.5061/dryad.h18931zwv). 3D renderings of glass brains require the Brainframe package, also developed by our group.
Users should clone this repository into their desired location and add all folders and subfolders to their MATLAB path.
The key script for generating results is Results_Script_CTVulnerability_clean.m, and each section can be run through one-by-one.
Users should not have to or attempt to modify other .m files, which are self-contained results- and figure-generating functions.
The only lines that are require modification are the external path locations, located at the top of this script:
- line 5: change "datapath" to name of the directory where large dependencies are located (downloaded from Dryad)
- line 6: change "figdirectory" to the name of the directory where figure files should be saved
- line 8: change "brainframedir" to the location of the Brainframe package
We also note that the "savenclose" variable controls whether to display items statically (0) or save them as uncompressed .tif images and then close them (1).