| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-HSV (1:1,750 for mono-, di-synaptic timepoints, 1:350 for trisynaptic)∗ | Dako | Cat# B011402-2 RRID: AB_2732870 |
| Chicken anti-GFP (1:750 for monosynaptic timepoints, 1:500 for disynaptic)∗ | Aves | Cat# GFP-1020 RRID: AB_10000240 |
| Donkey anti-rabbit AlexaFluor 647 (1:500 for mono-, di-synaptic timepoints, 1:250 for trisynaptic)∗ | Thermo Fisher Scientific | Cat# A31573 RRID: AB_2536183 |
| Donkey anti-chicken AlexaFluor 647 (1:400 for monosynaptic timepoints, 1:300 for disynaptic)∗ | Jackson ImmunoResearch | Cat# 703-606-155 RRID: AB_2340380 |
| Bacterial and virus strains | ||
| HSV-1 strain H129 recombinant VC22 | This paper | H129-VC22 (Princeton Viral Vector Core) |
| HSV-1 strain H129 recombinant 772 | This paper | H129-772 (Princeton Viral Vector Core) |
| PRV Bartha 152 | This paper | PRV-152 (Princeton Viral Vector Core) |
| Chemicals, peptides, and recombinant proteins | ||
| Mannitol | Sigma-Aldrich | M4125 |
| Isoflurane | VetOne | 501017 |
| Puralube, Pharmaderm | Pharmaderm | 37327 |
| Rimadyl (Carprofen) | Zoetis | 141-199 |
| CTB-555 | Sigma-Aldrich | C22843 |
| Ketamine | Vet One | #200-055 |
| Xylazine (Anased) | Akorn | 139-236 |
| 1× PBS | Thermo Fisher Scientific | 14190136 |
| Formalin (10%) | Fisher Scientific | 23-245685 |
| Paraformaldehyde (4%) | Fisher Scientific | AAJ19943 |
| Sodium azide | Sigma-Aldrich | S2002-500G |
| Triton X-100 | Sigma-Aldrich | T8787-50ML |
| Methanol | Carolina Biological Supply | 874195 |
| Hydrogen peroxide | Sigma-Aldrich | H1009-100M |
| Dimethyl sulfoxide (DMSO) | Fisher Scientific | D128-1 |
| Glycine | Sigma-Aldrich | 410225-50G |
| Donkey serum | EMD Millipore | S30-100ml |
| Tween-20 | Sigma-Aldrich | P9416-50ML |
| Heparin | Sigma-Aldrich | H3149-100KU |
| Dichloromethane (DCM) | Sigma-Aldrich | 270997-2L |
| Dibenzyl ether/benzyl ether (DBE) | Sigma-Aldrich | 108014-1KG |
| Super glue - for mounting brains | Loctite | 234796 |
| Krazy glue - for “suturing” after surgical incision | Elmer's | KG48348MR |
| Deposited data | ||
| Princeton Mouse Atlas (PMA) and injection data | Pisano et al., 2021 | https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links/ |
| HSV and PRV injection data aligned to Princeton Mouse Atlas | Pisano et al., 2021 | https://brainmaps.princeton.edu/2021/05/pisano_viral_tracing_injections/ |
| Experimental models: Organisms/strains | ||
| C57BL/6J mice, males and females, age 8–14 weeks | The Jackson Laboratory | 000664 |
| Software and algorithms | ||
| BrainPipe | Github.com/PrincetonUniversity/BrainPipe | zenodo.org/badge/latestdoi/149466560 |
| 3DUNet | Github.com/PrincetonUniversity/3dunet | zenodo.org/badge/latestdoi/157925214 |
| Pyalign | Github.com/PrincetonUniversity/pyalign | zenodo.org/badge/latestdoi/143018489 |
| Pyatlas | Github.com/PrincetonUniversity/pyatlas | zenodo.org/badge/latestdoi/131753598 |
| Python 3+ | (Van Rossum and Drake, 2009) | python.org |
| ImageJ | National Institutes of Health | imagej.net/software/fiji/ |
| Statsmodels 0.9.0 | (Seabold and Perktold, 2010) | statsmodels.org/stable/index.html |
| Blender | Blender | blender.org/ |
| ImSpector microscope controller software V 5.1.293 | LaVision BioTec | imspectordocs.readthedocs.io |
| Numpy 1.14.3 | (Oliphant, 2015) | numpy.org |
| Pandas 0.23.0 | (McKinney et al., 2010) | pandas.pydata.org |
| Matplotlib 2.2.2 | (Hunter, 2007) | matplotlib.org |
| Seaborn 0.9.0 | (Waskom et al., 2014) | seaborn.pydata.org |
| Scikit-Image 0.13.1 | (van der Walt et al., 2014) | scikit-image.org |
| SimpleITK 1.0.0 | (Lowekamp et al., 2013) | simpleITK.org |
| SciPy 1.1.0 | (Virtanen et al., 2020) | scipy.org |
| Scikit-Learn 0.19.1 | (Pedregosa et al., 2011) | scikit-learn.org |
| Other | ||
| Stereotaxic platform | David Kopf Instruments | Kopf Model 1900 |
| Soda lime glass | Kimble | 71900-10 |
| P-97 pipette puller | Sutter Instruments | P-97 |
| Dental drill | Osada | EXL-M40 |
| Burr drill bits | George Tiemann & Co | 160-1293-.24 (.24MM 1 3/4″ LONG 3/32 SHAFT) |
| Surgical body warmer | FHC | DC Temperature Control System |
| Surgifoam | Ethicon | #1972 |
| Black Resin | Formlabs | FLGPBK04 |
| Light-sheet microscope | LaVision BioTec | Ultramicroscope II |
| Emission filters | Semrock | FF01-525/39-25, FF01-609/54-25, FF01-680/42-25 |
| Dental cement | Parkell | S396 (C&B) |
| Kwik-Sil silicone sealant | World Precision Instruments | KWIK-SIL |
| Microinjection syringe pump system | World Precision Instruments | SYS-MICRO4 |
| Opaque magnets | Supermagnetman | D1005A-10 Parylene |
| 50 mL Eppendorf tubes | Fisher Scientific | 22-717-715 |
| 5 mL Eppendorf tubes | Fisher Scientific | 30119401 |
∗Note: Empiric antibody concentrations should be determined for each experiment (see Note at end of subsection viral injections).