KEY RESOURCE TABLE
| REAGENT OR RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| GFP Tag polyclonal 488 | Molecular probes | A-21311 |
| DAPI | Sigma | D9542 |
| Virus strains | ||
| AAV5-CAG-Flex-GCaMP6f-WPRE.SV40 | Chen et al., 2013 | 100835-AAV5 (Addgene) |
| AAV1-CAG-Flex-Jaws-KGC-Tdtomato-ER2 | Chuong et al., 2014 | 84446 (Addgene) |
| AAV1-CAG-FLEX-Tdtomato | Oh et al., 2014 | 51503-AAV1 (Addgene) |
| AAV1-EF1a-DIO-YFP | Deisseroth lab | 27056-AAV1 (Addgene) |
| AAV1-EF1a-DIO-hChR2(H134R)-eYFP-WRE-hGH | Deisseroth lab | 20298-AAV1 (Addgene) |
| AAV1-EF1a-DIO-hChR2(H134R)-mCherry-WPRE-HGHpA | Deisseroth lab | 20297-AAV1 (Addgene) |
| AAV-EF1a-DIO-mCherry-WPRE-HGHpA | Deisseroth lab | 20299-AAVrg (Addgene) |
| AAV-EF1a-DIO-hChR2(H134R)-mCherry-WPRE-HGHpA | Deisseroth lab | 20297-AAVrg (Addgene) |
| AAV pCAG-FLEX-tdTomato-WPREv | Deisseroth lab | 51503-AAVrg (Addgene) |
| rAAV2-CamKII-eYFP | UNC | N/A |
| retroAAV-CAG-Tdtomato | Boyden Lab | 59462-AAVrg |
| Experimental model | ||
| Tg(Arhgef6-cre)NL189Gsat/Mmucd | UCD | 034805-UCD |
| Software and algorithms | ||
| MATLAB | The MathWorks | https://www.mathworks.com/ |
| Fiji (ImageJ) | NIH | https://fiji.sc/ |
| Ilastik 1.3.2 | Sommer et al., 2011) | https://www.ilastik.org/ |
| Elastix | Elastix for image registration | https://elastix.lumc.nl/ |
| Imaris for 3D visualization and rendering | Oxford Instruments | https://imaris.oxinst.com/ |
| R for statistical computing | R project | https://www.r-project.org/ |
| BrainJ for image processing, registration, and analysis | This manuscript | https://www.cellularimaging.org/ |
| NIS-Elements for image acquisition | Nikon Instruments | https://www.microscope.healthcare.nikon.com/products/software/nis-elements |
| Illustrator | Adobe | https://www.adobe.com/products/illustrator.html |
| Constrained Non-negative Matrix Factorization (CNMF) | Pnevmatikakis et al., 2016 | N/A |
| Mosaic version 1.1.2.0 | Inscopix | https://www.inscopix.com |
| Mosaic version 1.2.0 | Inscopix | https://www.inscopix.com |
| Bonsai (x64) | Bonsai | https://bonsai-rx.org/ |
| Lowess algorithm | (Drai et al., 2000) | N/A |
| ROC analysis | (Cohen et al., 2012) | N/A |
| Clampex | Clampfit 10 | Molecular Devices | https://www.moleculardevices.com/ |
| GraphPad Prism 6 | GraphPad Prism | https://www.graphpad.com:443/ |
| Pipeline for image processing | Cellular Imaging, Zuckerman Institute | https://github.com/lahammond/BrainJ |