Experimental Models: Organisms/Strains |
Tg(elavl3:H2B-GCaMP6s) |
(Vladimirov et al., 2014) |
N/A |
Tg(gSA2AzGFF152B) |
(Takeuchi et al., 2015) |
N/A |
Tg(Huc:H2B-GCaMP6s; GAD1b:RFP) |
(Freeman et al., 2014; Satou et al, 2013) |
N/A |
Tg(UAS:GCaMP6s) |
(Filosa et al, 2016) |
N/A |
Software and Algorithms |
μManager |
Open Imaging |
https://micro-manager.org/ |
MATLAB (Behavioral and imaging analysis, modeling) |
MathWorks |
https://www.mathworks.com/products/matlab.html |
FIJI (ImageJ) (Image Processing) |
NIH |
http://fiji.sc |
Custom data-processing pipeline for LFM data |
(Prevedel et al, 2014) |
https://static-content.springer.com/esm/art%3A10.1038%2Fnmeth.2964/MediaObjects/41592_2014_BFnmeth2964_MOESM189_ESM.zip |
Demixed Principal Component Analysis (dPCA) |
(Kobak et al, 2016) |
https://github.com/machenslab/dPCA |
t-Distributed Stochastic Neighbor Embedding (t-SNE) |
(Maaten and Hinton, 2008) |
https://lvdmaaten.github.io/tsne/ |
Independent Component Analysis (FastICA) |
(Hyvarinen and Oja, 2000) |
https://research.ics.aalto.fi/ica/fastica/ |
Scanlmage |
(Pologruto et al, 2003) |
http://scanimage.vidriotechnologies.com/display/SIH/ScanImage+Home |
CalmAn-MATLAB |
(Giovannucci et al, 2019) |
https://github.com/flatironinstitute/CaImAn-MATLAB |
DeepLabCut 2.0 |
(Nath et al, 2019) |
https://github.com/AlexEMG/DeepLabCut |