KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited Data | ||
| Allen in situ data | Allan R Jones (Lein, 2007 #4147) | http://mouse.brain-map.org/ |
| Cell type specific whole brain map data | This paper | http://mouse.brainarchitecture.org/ost |
| Experimental Models: Organisms/Strains | ||
| Mouse: PV-IRES-Cre, (B6;129P2-Pvalbtm1(cre)Arbr/J) | Jackson Laboratory | Cat#008069 |
| Mouse: SST-IRES-Cre (Ssttm2.1(cre)Zjh/J) | Z. Josh Huang, Jackson Laboratory | Cat#013044 |
| Mouse: VIP-IRES-Cre (Viptm1(cre)Zjh/J) | Z. Josh Huang, Jackson Laboratory | Cat#010908 |
| Mouse: CR-IRES-Cre (B6(Cg)-Calb2tm1(cre)Zjh/J) | Z. Josh Huang, Jackson Laboratory | Cat#010774 |
| Mouse: nNOS-CreER-KI (B6;129S-Nos1tm1.1(cre/ERT2)Zjh/J) | Z. Josh Huang, Jackson Laboratory | Cat#014541 |
| Mouse: CCK-IRES-Cre (Ccktm1.1(cre)Zjh/J) | Z. Josh Huang, Jackson Laboratory | Cat#012706 |
| Mouse: Ai65 (B6;129S-Gt(ROSA)26Sortm65.1(CAG-tdTomato)Hze/J) | Z. Josh Huang, Jackson Laboratory | Cat#021875 |
| Mouse: SST-IRES-Flp (Ssttm3.1(flpo)Zjh/J) | Z. Josh Huang, Jackson Laboratory | Cat#028579 |
| Mouse: VIP-IRES-Flp (Viptm2.1(flpo)Zjh/J) | Z. Josh Huang, Jackson Laboratory | Cat#028578 |
| Mouse: CAG-LoxP-STOP-LoxP-H2B-GFP | Z. Josh Huang, (Taniguchi, 2011 #2169) | N/A |
| Software and Algorithms | ||
| STPT imaging stitching algorithm | Osten Laboratory | http://mouse.brainarchitecture.org/ost/ |
| Convolutional Neural network for cell counting | Osten Laboratory | http://mouse.brainarchitecture.org/ost/ |
| Elastix for image registration | Elastix | http://elastix.isi.uu.nl/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Volocity | Perkin Elmer | http://cellularimaging.perkinelmer.com/downloads/detail.php?id=14 |
| R for statistical computing | R project | https://www.r-project.org/ |
| Statistical algorithm | Osten Laboratory | http://mouse.brainarchitecture.org/ost/ |
| Whole brain flatmap | Larry Swanson | http://larrywswanson.com/?page_id=1415 |
| Python algorithms for digital flatmap | This paper | http://mouse.brainarchitecture.org/ost/ |
| Linear Discriminant Analysis | Python package Scikit-learn | http://scikit-learn.org/stable/ |
| Rate and spiking network simulation and analysis | This paper | https://github.com/xjwanglab |
| Illustrator | Adobe | http://www.adobe.com/products/illustrator.html |