| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| chicken anti-GFP | Invitrogen | Cat# A10262; RRID: AB_2534023 |
| chicken anti-Myc | Invitrogen | Cat# A21281; RRID: AB_2535826 |
| chicken anti-TH | Neuromics | Cat# CH23006; RRID: AB_2201403 |
| goat anti-ChAT | Millipore | Cat# AB144P; RRID: AB_2079751 |
| mouse anti-Myc | ATCC | Cat CRL-1729; RRID: CVCL_G671 |
| mouse anti-NeuN | Millipore | Cat# MAB377; RRID: AB_2298772 |
| mouse anti-V5 | Invitrogen | Cat# R960CUS; RRID: AB_2792973 |
| rabbit anti-RFP | Rockland | Cat# 600-401-379; RRID: AB_2209751 |
| Donkey anti-rabbit Cy3 | Jackson ImmunoResearch | Cat#711-165-152; RRID: AB_2307443 |
| Donkey anti-goat Cy5 | Invitrogen | Cat# A-21447; RRID: AB_2535864 |
| Donkey anti-chicken 488 | Jackson ImmunoResearch | Cat#703-545-155; RRID: AB_2340375 |
| Donkey anti-chicken Cy5 | Jackson ImmunoResearch | Cat#703-605-155; RRID: AB_2340379 |
| Donkey anti-goat 488 | Invitrogen | Cat# A-11055; RRID: AB_2534102 |
| Donkey anti-mouse 647 | Invitrogen | Cat# A-31571; RRID: AB_162542 |
| Donkey anti-mouse Cy3 | Invitrogen | Cat# A-31570; RRID: AB_2536180 |
| Donkey anti-mouse DyL405 | Jackson ImmunoResearch | Cat# 715-475-150; RRID: AB_2340839 |
| Donkey anti-goat DyL405 | Jackson ImmunoResearch | Cat# 705-475-147; RRID: AB_2340427 |
| Virus strains | ||
| AAV-flex-SynGFP | Pivetta et al., 2014 | N/A |
| AAV-ConFon-SynGFP | This study | N/A |
| AAV-flex-ReaChR-YFP | Capelli et al., 2017 | N/A |
| AAV-flex-Flp-H2B-V5 | Capelli et al., 2017 | N/A |
| AAV-H2B-10xMyc | Capelli et al., 2017 | N/A |
| AAV-flex-TdTomato | Capelli et al., 2017 | N/A |
| AAV-flex-Flp-H2B-V5 | Ruder et al., 2021 | N/A |
| AAV-flex-H2B-GFP | Ruder et al., 2021 | N/A |
| AAV-flex-H2B-TdTomato | Ruder et al., 2021 | N/A |
| AAV-flex-H2B-V5 | Ruder et al., 2021 | N/A |
| AAV-Con-Fon-ReaChR-Citrine-YFP | Ruder et al., 2021 | N/A |
| AAV-frt-H2B-TdTomato | This study | N/A |
| AAV-flex-GCaMP7f | Dana et al., 2019 | N/A |
| AAV-flex-stGtACR2-FusionRed | Mahn et al., 2018 | N/A |
| AAV-frt-stGtACR2-FusionRed | This study | N/A |
| AAV-flex-bReaChEs | Rajasethupathy et al., 2015 | N/A |
| Deposited data | ||
| CNMF-E | Pnevmatikakis et al., 2016; Zhou et al., 2018 | https://github.com/zhoupc/CNMF_E |
| Experimental models: organisms/strains | ||
| Mouse: vGlut2Cre: Slc17a6tm2(cre)Lowl | Jackson Laboratory | JAX:028863 |
| Mouse: Rbp4Cre: Tg(Rbp4-cre)KL100Gsat/Mmucd | MMRRC | MMRRC_031125-UCD |
| Mouse: vGATFLP: Slc32a1tm1.1(flpo)Hze | Jackson Laboratory | JAX:029591 |
| Software and algorithms | ||
| MATLAB (v2017b) | Mathworks | https://www.mathworks.com/RRID:SCR_001622 |
| GraphPad PRISM (v7.0) | GraphPad PRISM | https://www.graphpad.com:443/RRID:SCR_002798 |
| Python (v3.7) | Python | https://www.python.org/RRID:SCR_008394 |
| Knime (v3.3.1) | Knime | https://www.knime.com/RRID:SCR_006164 |
| CorelDraw (vX6 to X9) | Corel | https://www.coreldraw.com/en/RRID:SCR_014235 |
| Inscopix Data Acquisition Software (v1.2.1 and 1.4.1) | Inscopix | https://www.inscopix.com |
| Bonsai (v2.3) | NeuroGEARS | https://bonsai-rx.org |
| CinePlexStudio (v3.7.1) | Plexon | https://plexon.com |
| DeepLabCut | Mathis Lab (Mathis et al., 2018) | http://mackenziemathislab.org/deeplabcut |
| Other | ||
| 200mm: MFC_200/230-0.48_3.5mm_ZF1.25_FLT Mono Fiberoptic Cannula | Doric | https://neuro.doriclenses.com/ |
| 200mm: MFC_200/230-0.48_6mm_ZF1.25_FLT Mono Fiberoptic Cannula | Doric | https://neuro.doriclenses.com/ |
| ProView Lens Probe 0.6 mm diameter, ~7.3 mm length | Inscopix | https://www.inscopix.com |
| Microendoscope (Inscopix nVista 3.0) | Inscopix | https://www.inscopix.com |
| Wired 9-axis motion sensor | Champalimaud Foundation’s Scientific Hardware Platform | https://www.cf-hw.org |
| Harp WEAR basestation | Champalimaud Foundation’s Scientific Hardware Platform | https://www.cf-hw.org |
| Clock synchronizer | Champalimaud Foundation’s Scientific Hardware Platform | https://www.cf-hw.org |
| PlexBright Optogenetic Stimulation System | Plexon | https://plexon.com |
| OmniPlex Neural Recording Data Acquisition System | Plexon | https://plexon.com |
| FV1000 confocal microscope | Olympus | http://www.olympusconfocal.com/products/fv1000/index.html |
| ZEISS Axio Imager 2 | Zeiss | https://www.zeiss.com/microscopy/int/products/light-microscopes/axio-imager-2-for-biology.html |
| CSU-W1 Confocal Scanner Unit | Yokogawa | https://www.yokogawa.com/solutions/products-platforms/life-science/spinning-disk-confocal/csu-w1-confocal-scanner-unit/ |
| OxyletPro System - Treadmill | Panlab | https://www.harvardapparatus.com/catalog/product/view/id/9001/s/oxyletpro-system-treadmill-with-indirect-calorimetry/category/448/ |
| Ace 2 Area Scan Cameras | Basler AG | a2A1920-160umBAS |
| Pike Cameras | Allied Vision | https://www.alliedvision.com/en/support/technical-documentation/pike-documentation.html |
| Cobolt 06-MLD; 473nm; 100mW | HÜBNER Photonics | https://hubner-photonics.com/products/lasers/diode-lasers/06-01-series/ |
| Model 2650 Micropositioner | Kopf | https://kopfinstruments.com/product/model-2650-micropositioner/ |
| Mouse schemes | Zenodo, scidraw.io |
https://doi.org/10.5281/zenodo.3925993 https://doi.org/10.5281/zenodo.3925913 |
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