KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-Calbindin D-28k (Calb1) | Swant | Cat#CB38; RRID: AB_2721225 |
| Mouse monoclonal anti-NeuN | Millipore Sigma | Cat#MAB377; RRID: AB_2298772 |
| Rabbit polyclonal anti-Neurofilament, Medium, 160 kD (NF-160) | Abeam | Cat#AB9034; RRID: AB_306956 |
| Rabbit polyclonal anti-Parvalbumin | Swant | Cat#PV 25; RRID: AB_10000344 |
| Mouse monoclonal anti-Neurofilament H (SMI-32) | Covance | Cat#SMI-32R-100; RRID: AB_509997 |
| Mouse monoclonal anti-Myelin Basic Protein (SMI-99) | Covance | Cat#SMI-99P; RRID: AB_2564742 |
| Alexa Fluor 488 goat anti-rabbit | Thermo Fisher Scientific | Cat#A-11008; RRID: AB_10563748 |
| Alexa Fluor 594 goat anti-mouse | Thermo Fisher Scientific | Cat#A-11005; RRID: AB_2534073 |
| Bacterial and Virus Strains | ||
| AAV2/1.hSynapsin.EGFP.WPRE.bGH | UPenn Vector Core | Addgene AAV1; 105539; RRID:Addgene_105539 |
| AAV2/1.CAG.FLEX.EGFP.WPRE.bGH | UPenn Vector Core | Addgene AAV1; 51502; RRID: Addgene_51502 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Trimethoprim (TMP) | Sigma-Aldrich | T7883–5G |
| Tamoxifen (TAM) | Sigma-Aldrich | T5648–5G |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX: 000664 |
| Mouse: B6.Cg-Tg(A930038C07Rik-cre) 1Aibs/J, A930038C07Rik-Tg1-Cre | The Jackson Laboratory | JAX: 017346 |
| Mouse: Adcyap1–2A-Cre | Allen Institute for Brain Science | N/A |
| Mouse: B6;129S-Calb1tm2.1(cre)Hze/J,Calb1-IRES2-Cre | The Jackson Laboratory | JAX: 028532 |
| Mouse: B6.Cg-Calb1tm1.1(folA/EGFP/cre)Hze/J,Calb1-T2A-dgCre | The Jackson Laboratory | JAX: 023531 |
| Mouse: B6(Cg)-Calb2tm1(cre)Zjh/J,Calb2-IRES-Cre | The Jackson Laboratory | JAX: 010774 |
| Mouse: B6;129S-Cartpttm1.1(cre)Hze/J, Cart-IRES2-Cre | The Jackson Laboratory | JAX: 028533 |
| Mouse: STOCK Tg(Cartpt-cre)1Aibs/J, Cart-Tg1-Cre | The Jackson Laboratory | JAX: 009615 |
| Mouse: B6(Cg)-Ccktm2.1(cre/ERT2)Zjh/J, Cck-IRES-Cre | The Jackson Laboratory | JAX: 012706 |
| Mouse: B6;129S6-Chattm1(cre)Low1/j,Chat-IRES-Cre-neo | The Jackson Laboratory | JAX: 006410 |
| Mouse: STOCK Tg(Chma2-cre)OE25Gsat/Mmucd, Chma2-Cre_OE25 | MMRRC | MMRRC: 036502 |
| Mouse: STOCK Tg(Cnnm2-cre)KD18Gsat/Mmucd, Cnnm2-Cre_KD18 | MMRRC | MMRRC: 030951 |
| Mouse: Crh-IRES-Cre_BL | Bradford Lowell | N/A |
| Mouse: B6(Cg)-Crhtm1(cre)Zjh/J, Crh-IRES-Cre_ZJH | The Jackson Laboratory | JAX: 012704 |
| Mouse: B6.Cg-Ctgftm1.1(folA/cre)Hze/J, Ctgf-2A-dgCre | The Jackson Laboratory | JAX: 028535 |
| Mouse: B6(Cg)-Cux2tm3.1(cre/ERT2)Mull/Mmmh, Cux2-CreERT2 | MMRRC | MMRRC: 032779 |
| Mouse: B6(Cg)-Cux2tm1.1(cre)Mull/Mmmh, Cux2-IRES-Cre | MMRRC | MMRRC: 031778 |
| Mouse: STOCK Tg(Dbh-cre)KH212Gsat/Mmcd, Dbh-Cre_KH212 | MMRRC | MMRRC: 032081 |
| Mouse: STOCK Tg(Dlg3-cre)KG118Gsat/Mmucd, Dlg3-Cre_KG118 | MMRRC | MMRRC: 032809 |
| Mouse: Drd1a-Cre | Richard Palmiter | N/A |
| Mouse: STOCK Tg(Drd3-cre)KI196Gsat, Drd3-Cre_KI196 | MMRRC | MMRRC: 034610 |
| Mouse: STOCK Tg(Drd3-cre)KI198Gsat/Mmucd, Drd3-Cre_KI198 | MMRRC | MMRRC: 031741 |
| Mouse: STOCK Tg(Efr3a-cre)NO108Gsat/Mmucd, Efr3a-Cre_NO108 | MMRRC | MMRRC: 036660 |
| Mouse: B6.129S2-Emx1tm1(cre)Krj/J, Emx1-IRES-Cre | The Jackson Laboratory | JAX: 005628 |
| Mouse: B6.Cg-Erbb4tm1.1(cre/ERT2)Albs/j, Erbb4–2A-CreERT2 | The Jackson Laboratory | JAX: 012360 |
| Mouse: Esr1–2A-Cre | David Anderson | N/A |
| Mouse: B6;129S-Esr2tm1.1(cre)Hze/J, Esr2-IRES2-Cre | The Jackson Laboratory | JAX: 030158 |
| Mouse: B6(Cg)-Etv1tm1.1(cre/ERT2)Zjh/J, Etv1-CreERT2 | The Jackson Laboratory | JAX: 013048 |
| Mouse: B6;129S-Fezf1tm1.1(cre/folA)Hze/J, Fezf1–2A-dCre | The Jackson Laboratory | JAX: 013048 |
| Mouse: Fezf2-CreER | Z. Josh Huang | N/A |
| Mouse: B6.Cg-Foxp2tm1.1(cre/GFP)Rpa/J, Foxp2-IRES-Cre | The Jackson Laboratory | JAX: 030541 |
| Mouse: STOCK Gad2tm2(cre)Zjh/J, Gad2-IRES-Cre | The Jackson Laboratory | JAX: 010802 |
| Mouse: STOCK Tg(Gal-cre)KI87Gsat/Mmcd, Gal-Cre_KI87 | MMRRC | MMRRC: 031060 |
| Mouse: STOCK Tg(Colgalt2-cre) NF107Gsat/Mmucd, Glt25d2-Cre_NF107 | MMRRC | MMRRC: 036504 |
| Mouse: B6.Cg-Gnb4tm1.1(cre)Hze/J, Gnb4-IRES2-Cre | The Jackson Laboratory | JAX: 029587 |
| Mouse: B6.Cg-Gnb4tm1.1(cre/ERT2)Hze/J, Gnb4-IRES2-CreERT2 | The Jackson Laboratory | JAX: 030159 |
| Mouse: STOCK Tg(Gpr26-cre)KO250Gsat/Mmucd, Gpr26-Cre_K0250 | MMRRC | MMRRC: 033032 |
| Mouse: C57BL/6-Tg(Grik4-cre)G32–4Stl/J, Grik4-Cre | The Jackson Laboratory | JAX: 006474 |
| Mouse: STOCK Tg(Grm2-cre)MR90Gsat/Mmcd, Grm2-Cre_MR90 | MMRRC | MMRRC: 034611 |
| Mouse: STOCK Tg(Grp-cre)KH288Gsat/Mmucd, Grp-Cre_KH288 | MMRRC | MMRRC: 031183 |
| Mouse: B6;129S-Htr1atm1.1(cre)Hze/J, Htr1a-IRES2-Cre | The Jackson Laboratory | JAX: 030160 |
| Mouse: STOCK Tg(Htr2a-cre)KM207Gsat/Mmucd, Htr2a-Cre_KM207 | MMRRC | MMRRC: 031150 |
| Mouse: STOCK Tg(Htr3a-cre)NO152Gsat/Mmucd, Htr3a-Cre_NO152 | MMRRC | MMRRC: 036680 |
| Mouse: STOCK Jam2tm1.1(cre)Jrs/J, Jam2-Cre | The Jackson Laboratory | JAX: 031612 |
| Mouse: STOCK Tg(Kcnc2-Cre)K128Stl/LetJ, Kcnc2-Cre | The Jackson Laboratory | JAX: 008582 |
| Mouse: B6.129(SJL)-Kcng4tm1.1(Cre)Jrs/J, Kcng4-Cre | The Jackson Laboratory | JAX: 029414 |
| Mouse: B6.−129-Leprtm2(cre)Rck/J, Lepr-IRES-Cre | The Jackson Laboratory | JAX: 008320 |
| Mouse: Lypd6-Cre_KL156 | Nathaniel Heintz and Charles Gerfen | N/A |
| Mouse: B6.Cg-Ndnftm1.1(tolA/cre)Hze/J, Ndnf-IRES2-dgCre | The Jackson Laboratory | JAX: 028536 |
| Mouse: B6;129S-Nos1tm1.1(cre/ERT2)Zjh/J, Nos1-CreERT2 | The Jackson Laboratory | JAX: 014541 |
| Mouse: FVB-Tg(Nr5a1-cre)2Lowl/J, Nr5a1-Cre | The Jackson Laboratory | JAX: 006364 |
| Mouse: B6.Cg-Ntng2tm1.1(cre)Hze/J, Ntng2-IRES2-Cre | The Jackson Laboratory | JAX: 029588 |
| Mouse: B6;129S4-Ntrk1tm1(cre)Ltr/Mmucd, Ntrk1-IRES-Cre | MMRRC | MMRRC: 015500 |
| Mouse: B6.FVB(Cg)-Tg(Ntsr1-cre) GN220Gsat/Mmucd, Ntsr1-Cre_GN220 | MMRRC | MMRRC: 030648 |
| Mouse: B6.Cg-Nxph4tm1.1(cre/ERT2)Hze/J, Nxph4–2A-CreERT2 | The Jackson Laboratory | JAX: 022861 |
| Mouse: STOCK Tg(Oxtr-cre)ON66Gsat/Mmucd, Oxtr-Cre_ON66 | MMRRC | MMRRC: 036545 |
| Mouse: PB-mCitrine P038 | Shima et al., 2016 | N/A |
| Mouse: PB-mCitrine P170 | Shima et al., 2016 | N/A |
| Mouse: B6.Cg-Tg(Pcp2-cre)GN135Gsat/Mmucd, Pcp2-Cre_GN135 | MMRRC | MMRRC: 030868 |
| Mouse: B6;129S-Pdyntm1.1(cre/ERT2)Hze/J, Pdyn-T2A-CreERT2 | The Jackson Laboratory | JAX: 030197 |
| Mouse: STOCK Tg(Pdzk1ip1-cre) KD31Gsat/Mmucd, Pdzk1ip1-Cre_KD31 | MMRRC | MMRRC: 030851 |
| Mouse: B6;129S-Penktm2(cre)Hze/J, Penk-IRES2-Cre | The Jackson Laboratory | JAX: 025112 |
| Mouse: STOCK Tg(Plxnd1-cre)OG1Gsat/Mmucd, Plxnd1-Cre_OG1 | MMRRC | MMRRC: 036631 |
| Mouse: Plxnd1-CreER | Z. Josh Huang | N/A |
| Mouse: STOCK Tg(Pomc1-cre)16Lowl/J, Pomc-Cre_BL | The Jackson Laboratory | JAX: 005965 |
| Mouse: STOCK Tg(Ppp1r17-cre) NL146Gsat/Mmucd, Ppp1r17-Cre_NL146 | MMRRC | MMRRC: 036205 |
| Mouse: STOCK Tg(Prkcd-glc-1/CFP,-cre) EH124Gsat/Mmucd, Prkcd-GluCla-CFP-IRES-Cre_EH124 | MMRRC | MMRRC: 011559 |
| Mouse: B6;129P2-Pvalbtm1(cre)Arbr/J, Pvalb-IRES-Cre | The Jackson Laboratory | JAX: 008069 |
| Mouse: B6;129S-Rasgrf2tm1.1(cre/fola)Hze/J, Rasgrf2-T2A-dCre | The Jackson Laboratory | JAX: 022864 |
| Mouse: STOCK Tg(Rbp4-cre)KL100Gsat/Mmucd, Rbp4-Cre_KL100 | MMRRC | MMRRC: 031125 |
| Mouse: Rorb-IRES2-Cre-neo | Allen Institute for Brain Science | N/A |
| Mouse: B6;129S-Rorbtm1.1(cre)Hze/J, Rorb-IRES2-Cre | The Jackson Laboratory | JAX: 023526 |
| Mouse: B6;C3-Tg(Scnn1a-cre)2Aibs/J, Scnn1a-Tg2-Cre | The Jackson Laboratory | JAX: 009112 |
| Mouse: B6;C3-Tg(Scnn1a-cre)3Aibs/J, Scnn1a-Tg3-Cre | The Jackson Laboratory | JAX: 009613 |
| Mouse: Sdk2-CreER | Joshua Sanes | N/A |
| Mouse: STOCK Tg(Sim1-cre)KJ18Gsat/Mmucd, Sim1-Cre_KJ18 | MMRRC | MMRRC: 031742 |
| Mouse: STOCK Slc17a6tm2(cre)Lowl/J, Slc17a6-IRES-Cre | The Jackson Laboratory | JAX: 016963 |
| Mouse: B6;129S-Slc17a7tm1.1(cre)Hze/J, Slc17a7-IRES2-Cre | The Jackson Laboratory | JAX: 023527 |
| Mouse: Tg(Slc17a8-icre)1Edw/SealJ, Slc17a8-iCre | The Jackson Laboratory | JAX: 018147 |
| Mouse: B6;129S-Slc17a8tm1.1(cre)Hze/J, Slc17a8-IRES2-Cre | The Jackson Laboratory | JAX: 028534 |
| Mouse: STOCK Tg(Slc18a2-cre)OZ14Gsat/Mmcd, Slc18a2-Cre_OZ14 | MMRRC | MMRRC: 034814 |
| Mouse: STOCK Slc32a1tm2(cre)Lowl/J, Slc32a1-IRES-Cre | The Jackson Laboratory | JAX: 016962 |
| Mouse: STOCK Slc6a3tm1(cre)Xz/J, Slc6a3-Cre | The Jackson Laboratory | JAX: 020080 |
| Mouse: B6.Cg-Tg(Slc6a4-cre)ET33Gsat/Mmcd, Slc6a4-Cre_ET33 | MMRRC | MMRRC: 031028 |
| Mouse: STOCK Tg(Slc6a4-cre/ERT2) EZ13Gsat/Mmcd, Slc6a4-CreERT2_EZ13 | MMRRC | MMRRC: 030071 |
| Mouse: STOCK Tg(Slc6a5-cre)KF109Gsat/Mmucd, Slc6a5-Cre_KF109 | MMRRC | MMRRC: 030730 |
| Mouse: STOCK Ssttm2.1(cre)Zjh/J, Sst-IRES-Cre | The Jackson Laboratory | JAX: 013044 |
| Mouse: STOCK Tg(Syt17-cre)NO14Gsat/Mmucd, Syt17-Cre_NO14 | MMRRC | MMRRC: 034355 |
| Mouse: STOCK Tg(Syt6-cre)KI148Gsat/Mmucd, Syt6-Cre_KI148 | MMRRC | MMRRC: 032012 |
| Mouse: B6;129S-Tac1tm1.1(cre)Hze/J, Tac1-IRES2-Cre | The Jackson Laboratory | JAX: 021877 |
| Mouse: B6;129S-Tac2tm1.1(cre)Hze/J, Tac2-IRES2-Cre | The Jackson Laboratory | JAX: 021878 |
| Mouse: Tacr1-T2A-Cre | Daigle et al., 2018 | N/A |
| Mouse: B6;129S-Tac2tm1.1(cre)Hze/J, Tac2-IRES2-Cre | The Jackson Laboratory | JAX: 021878 |
| Mouse: B6.FVB(Cg)-Tg(Th-cre)FI172Gsat/Mmucd, Th-Cre_FI172 | MMRRC | MMRRC: 031029 |
| Mouse: FVB/N-Tg(Thy1-cre)1Vln/J, Thy1-Cre | The Jackson Laboratory | JAX: 006143 |
| Mouse: STOCK Tg(Tlx3-cre)PL56Gsat/Mmucd, Tlx3-Cre_PL56 | MMRRC | MMRRC: 041158 |
| Mouse: B6.Cg-Trib2tm1.1(cre/ERT2)Hze/J, Trib2-F2A-CreERT2 | The Jackson Laboratory | JAX: 022865 |
| Mouse: STOCK Viptm1(cre)Zjh/J, Vip-IRES-Cre | The Jackson Laboratory | JAX: 010908 |
| Mouse: STOCK Tg(Vipr2-cre)KE2Gsat/Mmucd, Vipr2-Cre_KE2 | MMRRC | MMRRC: 034281 |
| Mouse: STOCK Tg(Vipr2-cre)KE2Gsat/Mmucd, Vipr2-IRES2-Cre | The Jackson Laboratory | JAX: 031332 |
| Mouse: Vipr2-IRES2-Cre-neo | Allen Institute for Brain Science | N/A |
| Mouse: B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J, Ai14(RCL-tdT) | The Jackson Laboratory | JAX: 007914 |
| Mouse: B6.Cg-lgs7tm140.1(tetO-EGFP,CAG-tTA2)Hze/J, Ai140(TIT2L-GFP-ICL-tTA2) | The Jackson Laboratory | JAX: 030220 |
| Software and Algorithms | ||
| ITK-SNAP (http://itksnap.org) | Penn Image Computing and Science Laboratory (PICSL), Scientific Computing and Imaging Institute (SCI) | RRID:SCR_002010 |
| Insight Toolkit (ITK), SimplelTK (itk.org) | Kitware | RRID:SCR_001149 |
| Python 3.x (python.org) | Python Software Foundation | RRID:SCR_008394 |
| Anaconda | Anaconda | https://www.anaconda.com/ |
| NumPy (http://numpy.org) | NumPy Developers | RRID:SCR_008633 |
| pynrrd | Maarten H. Everts and contributors | https://github.com/mhe/pynrrd |
| pandas | NumFOCUS | https://pandas.pydata.org/ |
| h5py | The HDF Group (THG) | http://www.h5py.org/ |
| SciPy (http://scipy.org) | SciPy developers | RRID:SCR_008058 |
| pg8000 | Mathieu Fenniak | https://github.com/tlocke/pg8000 |
| Kakadu | Kakadu Software Pty Ltd | https://kakadusoftware.com/ |
| tinyXML | Lee Thomason | http://grinninglizard.com/tinyxml/ |
| Other | ||
| Allen Brain Reference Atlases | This paper | http://atlas.brain-map.org/ |
| Allen Mouse Brain Atlas | Lein et al., 2007 | http://mouse.brain-map.org |
| Allen Mouse Brain Connectivity Atlas | Oh et al., 2014; Harris et al., 2019 | http://connectivity.brain-map.org |
| Anatomic Reference Data | Allen Institute for Brain Science | http://connectivity.brain-map.org/static/referencedata |