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    Scientifica krueger burg lab software
    Krueger Burg Lab Software, supplied by Scientifica, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/image-processing+software+scanip/burg+krueger+lab+software/pm35063073-600-121-141
    Average 86 stars, based on 1 article reviews
    krueger burg lab software - by Bioz Stars, 2026-10
    86/100 stars

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    Related Articles

    Virus:

    Article Title: Vision-dependent specification of cell types and function in the developing cortex.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies VGLUT1 guinea pig polyclonal Millipore Sigma Cat# AB5905; RRID:AB_2301751 GAD65 mouse monoclonal Millipore Sigma Cat# MAB3521R; RRID:AB_94905 VGLUT2 guinea pig polyclonal Synaptic Systems Cat# 135404; RRID:AB_887884 NLGN2 guinea pig polyclonal Synaptic Systems Cat# 129205; RRID:AB_2619815 GABRA1 rabbit polyclonal Synaptic Systems Cat# 224203; RRID:AB_2232180 GABRG2 guinea pig polyclonal Synaptic Systems Cat# 224004; RRID:AB_10594245 VGAT rabbit polyclonal Synaptic Systems Cat# 131002; RRID:AB_887871 PSD95 rabbit polyclonal Thermo Fisher Cat# 516900; RRID:AB_2533914 SSCAM rabbit polyclonal Sigma Aldrich Cat# 2441; RRID:AB_477175 Goat anti-guinea pig polyclonal 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-mouse polyclonal 488 Invitrogen Cat# A11029; RRID:AB_138404 Goat anti-guinea pig 647 Life Technologies Cat# A21450; RRID:AB_141882 Goat anti-guinea pig 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-rabbit 488 Life Technologies Cat# A11008; RRID:AB_143165 Goat anti-mouse 568 Invitrogen Cat# A11031; RRID:AB_144696 Goat anti-rabbit 647 Invitrogen Cat# A21244; RRID:AB_2535812 Goat anti-rabbit 568 Invitrogen Cat# A11011; RRID:AB_143157 Chemicals, peptides, and recombinant proteins Prolong Gold Thermo Fisher Scientific Cat# P36930 Normal Goat Serum Sigma-Aldrich Cat# G6767 Paraformaldehyde Electron Microscopy Services Cat# 15714 2-methylbutane Sigma-Aldrich Cat# 277258 10X PBS Invitrogen Cat# AM9625 Tissue-Tek OCT compound, Sakura VMR Cat# 4583 RNAse inhibitor New England Biolabs Cat# M0314L 50x protease inhibitor Sigma-Aldrich Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 RNA later Thermo Fisher Scientific Cat# AM7020 Hibernate A minus calcium BrainBits Cat# HACA BSA (Bovine Serum Albumin) Sigma-Aldrich Cat# B6917 Ultrapure Dnase/Rnase Free distilled water Thermo Fisher Scientific Cat# 10-977-023 Ultrapure DEPC-treated water Thermo Fisher Scientific Cat# 10813012 Sucrose, Rnase, Dnase free Thermo Fisher Scientific Cat# AC419762500 D-Mannitol MilliporeSigma Cat# M9546-250G Igsf9b ACD Bio Cat# 832171-C3 Mdga1 ACD Bio Cat# 546411, 546411-C2 Nlgn2 ACD Bio Cat# 406681 Negative Control ACD Bio Cat# 320871 Positive Control ACD Bio Cat# 320881 probe diluent ACD Bio Cat# 300041 Slc17a7 ACD Bio Cat# 416631-C2, 416631, 416631-C3 Cdh13 ACD Bio Cat# 443251-C3 Chrm2 ACD Bio Cat# 495311-C2 (Continued on next page) e1 Cell 185, 311–327.e1–e11, January 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deptor ACD Bio Cat# 481561 - C3 Gad1 ACD Bio Cat# 400951-C2 Trpc6 ACD Bio Cat# 442951 Tshz2 ACD Bio Cat# 431061-C1 Bacterial and virus strains pGP-AAV-syn-jGCaMP7f-WPRE Addgene 104488-PHPeB Critical commercial assays Multiplex RNAscope v2 Cat# 323110 Chromium Single Cell Library and Gel Bead Kit v2 10X Genomics Cat# 120237 Chromium Single Cell A Chip Kit 10X Genomics Cat# 1000009 Deposited data Raw single-nucleus sequencing data NCBI GEO GEO: GSE190940 Visualized atlas Single Cell Portal Single Cell Portal SCP1664 Tuning kernels and SNR values for all neurons in 2P imaging Figshare https://figshare.com/articles/dataset/Vision- dependent_specification_of_cell_types_and_ function_in_the_developing_cortex/16992544 Experimental models: Organisms/strains Mouse: C57BL/6J JAX 664 Mouse: Igsf9b Gene trap in C57BL/6J background Gifted by the Krueger-Burg lab Gifted by the Krueger-Burg lab Software and algorithms Cell Ranger v2.1.0 10X Genomics www.support.10xgenomics.com/single-cell- gene-expression/software/overview/welcome FIJI (ImageJ) https://imagej.nih.gov/ij Zen Zeiss www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Linlab2 Scientifica https://www.scientifica.uk.com/products/ scientifica-linlab-2 MATLAB Mathworks mathworks.com Processing3 Processing Processing.org Suite2P https://suite2p.readthedocs.io/en/latest/ Cell Profiler v3.1.9 Broad Institute https://cellprofiler.org/ R R version 4.0.2 www.r-project.org/ Seurat 3.2.2 Stuart et al., 2019 https://github.com/satijalab/seurat Python 3.7 Anaconda3 www.anaconda.com SCANPY Wolf et al., 2018 https://scanpy.readthedocs.io/en/stable/ Scrublet Wolock et al., 2019 https://github.com/swolock/scrublet XGBoost Chen and Guestrin, 2016 https://xgboost.readthedocs.io/en/latest/ Harmony Korsunsky et al., 2019 https://github.com/immunogenomics/harmony Other LSM 880 Zeiss Resonant-Galvo scanning 2-photon microscope Neurolabware http://neurolabware.com/ Nanoject III Drummond Scientific https://www.drummondsci.com/microinjection/ nanoject-iii-programmable-nanoliter-injector/ Scientifica PatchStar Micromanipulator Scientifica https://www.scientifica.uk.com/products/ scientifica-patchstar-micromanipulator Chromium Controller 10X Genomics https://www.10xgenomics.com/instruments/ chromium-controller Leica CM1950 cryostat Leica https://www2.leicabiosystems.com/ Peel-A-Way Disposable Embedding Mold Polysciences Cat# 18646A-1 Black Rubberized Fabric Thorlabs Cat# BK5 ll Cell 185, 311–327.e1–e11, January 20, 2022 e2 Article ll Article .. Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, S. Lawrence Zipursky (lzipursky@mednet.ucla.edu).

    Multiplex Assay:

    Article Title: Vision-dependent specification of cell types and function in the developing cortex.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies VGLUT1 guinea pig polyclonal Millipore Sigma Cat# AB5905; RRID:AB_2301751 GAD65 mouse monoclonal Millipore Sigma Cat# MAB3521R; RRID:AB_94905 VGLUT2 guinea pig polyclonal Synaptic Systems Cat# 135404; RRID:AB_887884 NLGN2 guinea pig polyclonal Synaptic Systems Cat# 129205; RRID:AB_2619815 GABRA1 rabbit polyclonal Synaptic Systems Cat# 224203; RRID:AB_2232180 GABRG2 guinea pig polyclonal Synaptic Systems Cat# 224004; RRID:AB_10594245 VGAT rabbit polyclonal Synaptic Systems Cat# 131002; RRID:AB_887871 PSD95 rabbit polyclonal Thermo Fisher Cat# 516900; RRID:AB_2533914 SSCAM rabbit polyclonal Sigma Aldrich Cat# 2441; RRID:AB_477175 Goat anti-guinea pig polyclonal 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-mouse polyclonal 488 Invitrogen Cat# A11029; RRID:AB_138404 Goat anti-guinea pig 647 Life Technologies Cat# A21450; RRID:AB_141882 Goat anti-guinea pig 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-rabbit 488 Life Technologies Cat# A11008; RRID:AB_143165 Goat anti-mouse 568 Invitrogen Cat# A11031; RRID:AB_144696 Goat anti-rabbit 647 Invitrogen Cat# A21244; RRID:AB_2535812 Goat anti-rabbit 568 Invitrogen Cat# A11011; RRID:AB_143157 Chemicals, peptides, and recombinant proteins Prolong Gold Thermo Fisher Scientific Cat# P36930 Normal Goat Serum Sigma-Aldrich Cat# G6767 Paraformaldehyde Electron Microscopy Services Cat# 15714 2-methylbutane Sigma-Aldrich Cat# 277258 10X PBS Invitrogen Cat# AM9625 Tissue-Tek OCT compound, Sakura VMR Cat# 4583 RNAse inhibitor New England Biolabs Cat# M0314L 50x protease inhibitor Sigma-Aldrich Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 RNA later Thermo Fisher Scientific Cat# AM7020 Hibernate A minus calcium BrainBits Cat# HACA BSA (Bovine Serum Albumin) Sigma-Aldrich Cat# B6917 Ultrapure Dnase/Rnase Free distilled water Thermo Fisher Scientific Cat# 10-977-023 Ultrapure DEPC-treated water Thermo Fisher Scientific Cat# 10813012 Sucrose, Rnase, Dnase free Thermo Fisher Scientific Cat# AC419762500 D-Mannitol MilliporeSigma Cat# M9546-250G Igsf9b ACD Bio Cat# 832171-C3 Mdga1 ACD Bio Cat# 546411, 546411-C2 Nlgn2 ACD Bio Cat# 406681 Negative Control ACD Bio Cat# 320871 Positive Control ACD Bio Cat# 320881 probe diluent ACD Bio Cat# 300041 Slc17a7 ACD Bio Cat# 416631-C2, 416631, 416631-C3 Cdh13 ACD Bio Cat# 443251-C3 Chrm2 ACD Bio Cat# 495311-C2 (Continued on next page) e1 Cell 185, 311–327.e1–e11, January 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deptor ACD Bio Cat# 481561 - C3 Gad1 ACD Bio Cat# 400951-C2 Trpc6 ACD Bio Cat# 442951 Tshz2 ACD Bio Cat# 431061-C1 Bacterial and virus strains pGP-AAV-syn-jGCaMP7f-WPRE Addgene 104488-PHPeB Critical commercial assays Multiplex RNAscope v2 Cat# 323110 Chromium Single Cell Library and Gel Bead Kit v2 10X Genomics Cat# 120237 Chromium Single Cell A Chip Kit 10X Genomics Cat# 1000009 Deposited data Raw single-nucleus sequencing data NCBI GEO GEO: GSE190940 Visualized atlas Single Cell Portal Single Cell Portal SCP1664 Tuning kernels and SNR values for all neurons in 2P imaging Figshare https://figshare.com/articles/dataset/Vision- dependent_specification_of_cell_types_and_ function_in_the_developing_cortex/16992544 Experimental models: Organisms/strains Mouse: C57BL/6J JAX 664 Mouse: Igsf9b Gene trap in C57BL/6J background Gifted by the Krueger-Burg lab Gifted by the Krueger-Burg lab Software and algorithms Cell Ranger v2.1.0 10X Genomics www.support.10xgenomics.com/single-cell- gene-expression/software/overview/welcome FIJI (ImageJ) https://imagej.nih.gov/ij Zen Zeiss www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Linlab2 Scientifica https://www.scientifica.uk.com/products/ scientifica-linlab-2 MATLAB Mathworks mathworks.com Processing3 Processing Processing.org Suite2P https://suite2p.readthedocs.io/en/latest/ Cell Profiler v3.1.9 Broad Institute https://cellprofiler.org/ R R version 4.0.2 www.r-project.org/ Seurat 3.2.2 Stuart et al., 2019 https://github.com/satijalab/seurat Python 3.7 Anaconda3 www.anaconda.com SCANPY Wolf et al., 2018 https://scanpy.readthedocs.io/en/stable/ Scrublet Wolock et al., 2019 https://github.com/swolock/scrublet XGBoost Chen and Guestrin, 2016 https://xgboost.readthedocs.io/en/latest/ Harmony Korsunsky et al., 2019 https://github.com/immunogenomics/harmony Other LSM 880 Zeiss Resonant-Galvo scanning 2-photon microscope Neurolabware http://neurolabware.com/ Nanoject III Drummond Scientific https://www.drummondsci.com/microinjection/ nanoject-iii-programmable-nanoliter-injector/ Scientifica PatchStar Micromanipulator Scientifica https://www.scientifica.uk.com/products/ scientifica-patchstar-micromanipulator Chromium Controller 10X Genomics https://www.10xgenomics.com/instruments/ chromium-controller Leica CM1950 cryostat Leica https://www2.leicabiosystems.com/ Peel-A-Way Disposable Embedding Mold Polysciences Cat# 18646A-1 Black Rubberized Fabric Thorlabs Cat# BK5 ll Cell 185, 311–327.e1–e11, January 20, 2022 e2 Article ll Article .. Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, S. Lawrence Zipursky (lzipursky@mednet.ucla.edu).

    RNAscope:

    Article Title: Vision-dependent specification of cell types and function in the developing cortex.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies VGLUT1 guinea pig polyclonal Millipore Sigma Cat# AB5905; RRID:AB_2301751 GAD65 mouse monoclonal Millipore Sigma Cat# MAB3521R; RRID:AB_94905 VGLUT2 guinea pig polyclonal Synaptic Systems Cat# 135404; RRID:AB_887884 NLGN2 guinea pig polyclonal Synaptic Systems Cat# 129205; RRID:AB_2619815 GABRA1 rabbit polyclonal Synaptic Systems Cat# 224203; RRID:AB_2232180 GABRG2 guinea pig polyclonal Synaptic Systems Cat# 224004; RRID:AB_10594245 VGAT rabbit polyclonal Synaptic Systems Cat# 131002; RRID:AB_887871 PSD95 rabbit polyclonal Thermo Fisher Cat# 516900; RRID:AB_2533914 SSCAM rabbit polyclonal Sigma Aldrich Cat# 2441; RRID:AB_477175 Goat anti-guinea pig polyclonal 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-mouse polyclonal 488 Invitrogen Cat# A11029; RRID:AB_138404 Goat anti-guinea pig 647 Life Technologies Cat# A21450; RRID:AB_141882 Goat anti-guinea pig 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-rabbit 488 Life Technologies Cat# A11008; RRID:AB_143165 Goat anti-mouse 568 Invitrogen Cat# A11031; RRID:AB_144696 Goat anti-rabbit 647 Invitrogen Cat# A21244; RRID:AB_2535812 Goat anti-rabbit 568 Invitrogen Cat# A11011; RRID:AB_143157 Chemicals, peptides, and recombinant proteins Prolong Gold Thermo Fisher Scientific Cat# P36930 Normal Goat Serum Sigma-Aldrich Cat# G6767 Paraformaldehyde Electron Microscopy Services Cat# 15714 2-methylbutane Sigma-Aldrich Cat# 277258 10X PBS Invitrogen Cat# AM9625 Tissue-Tek OCT compound, Sakura VMR Cat# 4583 RNAse inhibitor New England Biolabs Cat# M0314L 50x protease inhibitor Sigma-Aldrich Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 RNA later Thermo Fisher Scientific Cat# AM7020 Hibernate A minus calcium BrainBits Cat# HACA BSA (Bovine Serum Albumin) Sigma-Aldrich Cat# B6917 Ultrapure Dnase/Rnase Free distilled water Thermo Fisher Scientific Cat# 10-977-023 Ultrapure DEPC-treated water Thermo Fisher Scientific Cat# 10813012 Sucrose, Rnase, Dnase free Thermo Fisher Scientific Cat# AC419762500 D-Mannitol MilliporeSigma Cat# M9546-250G Igsf9b ACD Bio Cat# 832171-C3 Mdga1 ACD Bio Cat# 546411, 546411-C2 Nlgn2 ACD Bio Cat# 406681 Negative Control ACD Bio Cat# 320871 Positive Control ACD Bio Cat# 320881 probe diluent ACD Bio Cat# 300041 Slc17a7 ACD Bio Cat# 416631-C2, 416631, 416631-C3 Cdh13 ACD Bio Cat# 443251-C3 Chrm2 ACD Bio Cat# 495311-C2 (Continued on next page) e1 Cell 185, 311–327.e1–e11, January 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deptor ACD Bio Cat# 481561 - C3 Gad1 ACD Bio Cat# 400951-C2 Trpc6 ACD Bio Cat# 442951 Tshz2 ACD Bio Cat# 431061-C1 Bacterial and virus strains pGP-AAV-syn-jGCaMP7f-WPRE Addgene 104488-PHPeB Critical commercial assays Multiplex RNAscope v2 Cat# 323110 Chromium Single Cell Library and Gel Bead Kit v2 10X Genomics Cat# 120237 Chromium Single Cell A Chip Kit 10X Genomics Cat# 1000009 Deposited data Raw single-nucleus sequencing data NCBI GEO GEO: GSE190940 Visualized atlas Single Cell Portal Single Cell Portal SCP1664 Tuning kernels and SNR values for all neurons in 2P imaging Figshare https://figshare.com/articles/dataset/Vision- dependent_specification_of_cell_types_and_ function_in_the_developing_cortex/16992544 Experimental models: Organisms/strains Mouse: C57BL/6J JAX 664 Mouse: Igsf9b Gene trap in C57BL/6J background Gifted by the Krueger-Burg lab Gifted by the Krueger-Burg lab Software and algorithms Cell Ranger v2.1.0 10X Genomics www.support.10xgenomics.com/single-cell- gene-expression/software/overview/welcome FIJI (ImageJ) https://imagej.nih.gov/ij Zen Zeiss www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Linlab2 Scientifica https://www.scientifica.uk.com/products/ scientifica-linlab-2 MATLAB Mathworks mathworks.com Processing3 Processing Processing.org Suite2P https://suite2p.readthedocs.io/en/latest/ Cell Profiler v3.1.9 Broad Institute https://cellprofiler.org/ R R version 4.0.2 www.r-project.org/ Seurat 3.2.2 Stuart et al., 2019 https://github.com/satijalab/seurat Python 3.7 Anaconda3 www.anaconda.com SCANPY Wolf et al., 2018 https://scanpy.readthedocs.io/en/stable/ Scrublet Wolock et al., 2019 https://github.com/swolock/scrublet XGBoost Chen and Guestrin, 2016 https://xgboost.readthedocs.io/en/latest/ Harmony Korsunsky et al., 2019 https://github.com/immunogenomics/harmony Other LSM 880 Zeiss Resonant-Galvo scanning 2-photon microscope Neurolabware http://neurolabware.com/ Nanoject III Drummond Scientific https://www.drummondsci.com/microinjection/ nanoject-iii-programmable-nanoliter-injector/ Scientifica PatchStar Micromanipulator Scientifica https://www.scientifica.uk.com/products/ scientifica-patchstar-micromanipulator Chromium Controller 10X Genomics https://www.10xgenomics.com/instruments/ chromium-controller Leica CM1950 cryostat Leica https://www2.leicabiosystems.com/ Peel-A-Way Disposable Embedding Mold Polysciences Cat# 18646A-1 Black Rubberized Fabric Thorlabs Cat# BK5 ll Cell 185, 311–327.e1–e11, January 20, 2022 e2 Article ll Article .. Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, S. Lawrence Zipursky (lzipursky@mednet.ucla.edu).

    Single Cell:

    Article Title: Vision-dependent specification of cell types and function in the developing cortex.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies VGLUT1 guinea pig polyclonal Millipore Sigma Cat# AB5905; RRID:AB_2301751 GAD65 mouse monoclonal Millipore Sigma Cat# MAB3521R; RRID:AB_94905 VGLUT2 guinea pig polyclonal Synaptic Systems Cat# 135404; RRID:AB_887884 NLGN2 guinea pig polyclonal Synaptic Systems Cat# 129205; RRID:AB_2619815 GABRA1 rabbit polyclonal Synaptic Systems Cat# 224203; RRID:AB_2232180 GABRG2 guinea pig polyclonal Synaptic Systems Cat# 224004; RRID:AB_10594245 VGAT rabbit polyclonal Synaptic Systems Cat# 131002; RRID:AB_887871 PSD95 rabbit polyclonal Thermo Fisher Cat# 516900; RRID:AB_2533914 SSCAM rabbit polyclonal Sigma Aldrich Cat# 2441; RRID:AB_477175 Goat anti-guinea pig polyclonal 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-mouse polyclonal 488 Invitrogen Cat# A11029; RRID:AB_138404 Goat anti-guinea pig 647 Life Technologies Cat# A21450; RRID:AB_141882 Goat anti-guinea pig 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-rabbit 488 Life Technologies Cat# A11008; RRID:AB_143165 Goat anti-mouse 568 Invitrogen Cat# A11031; RRID:AB_144696 Goat anti-rabbit 647 Invitrogen Cat# A21244; RRID:AB_2535812 Goat anti-rabbit 568 Invitrogen Cat# A11011; RRID:AB_143157 Chemicals, peptides, and recombinant proteins Prolong Gold Thermo Fisher Scientific Cat# P36930 Normal Goat Serum Sigma-Aldrich Cat# G6767 Paraformaldehyde Electron Microscopy Services Cat# 15714 2-methylbutane Sigma-Aldrich Cat# 277258 10X PBS Invitrogen Cat# AM9625 Tissue-Tek OCT compound, Sakura VMR Cat# 4583 RNAse inhibitor New England Biolabs Cat# M0314L 50x protease inhibitor Sigma-Aldrich Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 RNA later Thermo Fisher Scientific Cat# AM7020 Hibernate A minus calcium BrainBits Cat# HACA BSA (Bovine Serum Albumin) Sigma-Aldrich Cat# B6917 Ultrapure Dnase/Rnase Free distilled water Thermo Fisher Scientific Cat# 10-977-023 Ultrapure DEPC-treated water Thermo Fisher Scientific Cat# 10813012 Sucrose, Rnase, Dnase free Thermo Fisher Scientific Cat# AC419762500 D-Mannitol MilliporeSigma Cat# M9546-250G Igsf9b ACD Bio Cat# 832171-C3 Mdga1 ACD Bio Cat# 546411, 546411-C2 Nlgn2 ACD Bio Cat# 406681 Negative Control ACD Bio Cat# 320871 Positive Control ACD Bio Cat# 320881 probe diluent ACD Bio Cat# 300041 Slc17a7 ACD Bio Cat# 416631-C2, 416631, 416631-C3 Cdh13 ACD Bio Cat# 443251-C3 Chrm2 ACD Bio Cat# 495311-C2 (Continued on next page) e1 Cell 185, 311–327.e1–e11, January 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deptor ACD Bio Cat# 481561 - C3 Gad1 ACD Bio Cat# 400951-C2 Trpc6 ACD Bio Cat# 442951 Tshz2 ACD Bio Cat# 431061-C1 Bacterial and virus strains pGP-AAV-syn-jGCaMP7f-WPRE Addgene 104488-PHPeB Critical commercial assays Multiplex RNAscope v2 Cat# 323110 Chromium Single Cell Library and Gel Bead Kit v2 10X Genomics Cat# 120237 Chromium Single Cell A Chip Kit 10X Genomics Cat# 1000009 Deposited data Raw single-nucleus sequencing data NCBI GEO GEO: GSE190940 Visualized atlas Single Cell Portal Single Cell Portal SCP1664 Tuning kernels and SNR values for all neurons in 2P imaging Figshare https://figshare.com/articles/dataset/Vision- dependent_specification_of_cell_types_and_ function_in_the_developing_cortex/16992544 Experimental models: Organisms/strains Mouse: C57BL/6J JAX 664 Mouse: Igsf9b Gene trap in C57BL/6J background Gifted by the Krueger-Burg lab Gifted by the Krueger-Burg lab Software and algorithms Cell Ranger v2.1.0 10X Genomics www.support.10xgenomics.com/single-cell- gene-expression/software/overview/welcome FIJI (ImageJ) https://imagej.nih.gov/ij Zen Zeiss www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Linlab2 Scientifica https://www.scientifica.uk.com/products/ scientifica-linlab-2 MATLAB Mathworks mathworks.com Processing3 Processing Processing.org Suite2P https://suite2p.readthedocs.io/en/latest/ Cell Profiler v3.1.9 Broad Institute https://cellprofiler.org/ R R version 4.0.2 www.r-project.org/ Seurat 3.2.2 Stuart et al., 2019 https://github.com/satijalab/seurat Python 3.7 Anaconda3 www.anaconda.com SCANPY Wolf et al., 2018 https://scanpy.readthedocs.io/en/stable/ Scrublet Wolock et al., 2019 https://github.com/swolock/scrublet XGBoost Chen and Guestrin, 2016 https://xgboost.readthedocs.io/en/latest/ Harmony Korsunsky et al., 2019 https://github.com/immunogenomics/harmony Other LSM 880 Zeiss Resonant-Galvo scanning 2-photon microscope Neurolabware http://neurolabware.com/ Nanoject III Drummond Scientific https://www.drummondsci.com/microinjection/ nanoject-iii-programmable-nanoliter-injector/ Scientifica PatchStar Micromanipulator Scientifica https://www.scientifica.uk.com/products/ scientifica-patchstar-micromanipulator Chromium Controller 10X Genomics https://www.10xgenomics.com/instruments/ chromium-controller Leica CM1950 cryostat Leica https://www2.leicabiosystems.com/ Peel-A-Way Disposable Embedding Mold Polysciences Cat# 18646A-1 Black Rubberized Fabric Thorlabs Cat# BK5 ll Cell 185, 311–327.e1–e11, January 20, 2022 e2 Article ll Article .. Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, S. Lawrence Zipursky (lzipursky@mednet.ucla.edu).

    Sequencing:

    Article Title: Vision-dependent specification of cell types and function in the developing cortex.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies VGLUT1 guinea pig polyclonal Millipore Sigma Cat# AB5905; RRID:AB_2301751 GAD65 mouse monoclonal Millipore Sigma Cat# MAB3521R; RRID:AB_94905 VGLUT2 guinea pig polyclonal Synaptic Systems Cat# 135404; RRID:AB_887884 NLGN2 guinea pig polyclonal Synaptic Systems Cat# 129205; RRID:AB_2619815 GABRA1 rabbit polyclonal Synaptic Systems Cat# 224203; RRID:AB_2232180 GABRG2 guinea pig polyclonal Synaptic Systems Cat# 224004; RRID:AB_10594245 VGAT rabbit polyclonal Synaptic Systems Cat# 131002; RRID:AB_887871 PSD95 rabbit polyclonal Thermo Fisher Cat# 516900; RRID:AB_2533914 SSCAM rabbit polyclonal Sigma Aldrich Cat# 2441; RRID:AB_477175 Goat anti-guinea pig polyclonal 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-mouse polyclonal 488 Invitrogen Cat# A11029; RRID:AB_138404 Goat anti-guinea pig 647 Life Technologies Cat# A21450; RRID:AB_141882 Goat anti-guinea pig 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-rabbit 488 Life Technologies Cat# A11008; RRID:AB_143165 Goat anti-mouse 568 Invitrogen Cat# A11031; RRID:AB_144696 Goat anti-rabbit 647 Invitrogen Cat# A21244; RRID:AB_2535812 Goat anti-rabbit 568 Invitrogen Cat# A11011; RRID:AB_143157 Chemicals, peptides, and recombinant proteins Prolong Gold Thermo Fisher Scientific Cat# P36930 Normal Goat Serum Sigma-Aldrich Cat# G6767 Paraformaldehyde Electron Microscopy Services Cat# 15714 2-methylbutane Sigma-Aldrich Cat# 277258 10X PBS Invitrogen Cat# AM9625 Tissue-Tek OCT compound, Sakura VMR Cat# 4583 RNAse inhibitor New England Biolabs Cat# M0314L 50x protease inhibitor Sigma-Aldrich Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 RNA later Thermo Fisher Scientific Cat# AM7020 Hibernate A minus calcium BrainBits Cat# HACA BSA (Bovine Serum Albumin) Sigma-Aldrich Cat# B6917 Ultrapure Dnase/Rnase Free distilled water Thermo Fisher Scientific Cat# 10-977-023 Ultrapure DEPC-treated water Thermo Fisher Scientific Cat# 10813012 Sucrose, Rnase, Dnase free Thermo Fisher Scientific Cat# AC419762500 D-Mannitol MilliporeSigma Cat# M9546-250G Igsf9b ACD Bio Cat# 832171-C3 Mdga1 ACD Bio Cat# 546411, 546411-C2 Nlgn2 ACD Bio Cat# 406681 Negative Control ACD Bio Cat# 320871 Positive Control ACD Bio Cat# 320881 probe diluent ACD Bio Cat# 300041 Slc17a7 ACD Bio Cat# 416631-C2, 416631, 416631-C3 Cdh13 ACD Bio Cat# 443251-C3 Chrm2 ACD Bio Cat# 495311-C2 (Continued on next page) e1 Cell 185, 311–327.e1–e11, January 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deptor ACD Bio Cat# 481561 - C3 Gad1 ACD Bio Cat# 400951-C2 Trpc6 ACD Bio Cat# 442951 Tshz2 ACD Bio Cat# 431061-C1 Bacterial and virus strains pGP-AAV-syn-jGCaMP7f-WPRE Addgene 104488-PHPeB Critical commercial assays Multiplex RNAscope v2 Cat# 323110 Chromium Single Cell Library and Gel Bead Kit v2 10X Genomics Cat# 120237 Chromium Single Cell A Chip Kit 10X Genomics Cat# 1000009 Deposited data Raw single-nucleus sequencing data NCBI GEO GEO: GSE190940 Visualized atlas Single Cell Portal Single Cell Portal SCP1664 Tuning kernels and SNR values for all neurons in 2P imaging Figshare https://figshare.com/articles/dataset/Vision- dependent_specification_of_cell_types_and_ function_in_the_developing_cortex/16992544 Experimental models: Organisms/strains Mouse: C57BL/6J JAX 664 Mouse: Igsf9b Gene trap in C57BL/6J background Gifted by the Krueger-Burg lab Gifted by the Krueger-Burg lab Software and algorithms Cell Ranger v2.1.0 10X Genomics www.support.10xgenomics.com/single-cell- gene-expression/software/overview/welcome FIJI (ImageJ) https://imagej.nih.gov/ij Zen Zeiss www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Linlab2 Scientifica https://www.scientifica.uk.com/products/ scientifica-linlab-2 MATLAB Mathworks mathworks.com Processing3 Processing Processing.org Suite2P https://suite2p.readthedocs.io/en/latest/ Cell Profiler v3.1.9 Broad Institute https://cellprofiler.org/ R R version 4.0.2 www.r-project.org/ Seurat 3.2.2 Stuart et al., 2019 https://github.com/satijalab/seurat Python 3.7 Anaconda3 www.anaconda.com SCANPY Wolf et al., 2018 https://scanpy.readthedocs.io/en/stable/ Scrublet Wolock et al., 2019 https://github.com/swolock/scrublet XGBoost Chen and Guestrin, 2016 https://xgboost.readthedocs.io/en/latest/ Harmony Korsunsky et al., 2019 https://github.com/immunogenomics/harmony Other LSM 880 Zeiss Resonant-Galvo scanning 2-photon microscope Neurolabware http://neurolabware.com/ Nanoject III Drummond Scientific https://www.drummondsci.com/microinjection/ nanoject-iii-programmable-nanoliter-injector/ Scientifica PatchStar Micromanipulator Scientifica https://www.scientifica.uk.com/products/ scientifica-patchstar-micromanipulator Chromium Controller 10X Genomics https://www.10xgenomics.com/instruments/ chromium-controller Leica CM1950 cryostat Leica https://www2.leicabiosystems.com/ Peel-A-Way Disposable Embedding Mold Polysciences Cat# 18646A-1 Black Rubberized Fabric Thorlabs Cat# BK5 ll Cell 185, 311–327.e1–e11, January 20, 2022 e2 Article ll Article .. Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, S. Lawrence Zipursky (lzipursky@mednet.ucla.edu).

    Imaging:

    Article Title: Vision-dependent specification of cell types and function in the developing cortex.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies VGLUT1 guinea pig polyclonal Millipore Sigma Cat# AB5905; RRID:AB_2301751 GAD65 mouse monoclonal Millipore Sigma Cat# MAB3521R; RRID:AB_94905 VGLUT2 guinea pig polyclonal Synaptic Systems Cat# 135404; RRID:AB_887884 NLGN2 guinea pig polyclonal Synaptic Systems Cat# 129205; RRID:AB_2619815 GABRA1 rabbit polyclonal Synaptic Systems Cat# 224203; RRID:AB_2232180 GABRG2 guinea pig polyclonal Synaptic Systems Cat# 224004; RRID:AB_10594245 VGAT rabbit polyclonal Synaptic Systems Cat# 131002; RRID:AB_887871 PSD95 rabbit polyclonal Thermo Fisher Cat# 516900; RRID:AB_2533914 SSCAM rabbit polyclonal Sigma Aldrich Cat# 2441; RRID:AB_477175 Goat anti-guinea pig polyclonal 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-mouse polyclonal 488 Invitrogen Cat# A11029; RRID:AB_138404 Goat anti-guinea pig 647 Life Technologies Cat# A21450; RRID:AB_141882 Goat anti-guinea pig 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-rabbit 488 Life Technologies Cat# A11008; RRID:AB_143165 Goat anti-mouse 568 Invitrogen Cat# A11031; RRID:AB_144696 Goat anti-rabbit 647 Invitrogen Cat# A21244; RRID:AB_2535812 Goat anti-rabbit 568 Invitrogen Cat# A11011; RRID:AB_143157 Chemicals, peptides, and recombinant proteins Prolong Gold Thermo Fisher Scientific Cat# P36930 Normal Goat Serum Sigma-Aldrich Cat# G6767 Paraformaldehyde Electron Microscopy Services Cat# 15714 2-methylbutane Sigma-Aldrich Cat# 277258 10X PBS Invitrogen Cat# AM9625 Tissue-Tek OCT compound, Sakura VMR Cat# 4583 RNAse inhibitor New England Biolabs Cat# M0314L 50x protease inhibitor Sigma-Aldrich Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 RNA later Thermo Fisher Scientific Cat# AM7020 Hibernate A minus calcium BrainBits Cat# HACA BSA (Bovine Serum Albumin) Sigma-Aldrich Cat# B6917 Ultrapure Dnase/Rnase Free distilled water Thermo Fisher Scientific Cat# 10-977-023 Ultrapure DEPC-treated water Thermo Fisher Scientific Cat# 10813012 Sucrose, Rnase, Dnase free Thermo Fisher Scientific Cat# AC419762500 D-Mannitol MilliporeSigma Cat# M9546-250G Igsf9b ACD Bio Cat# 832171-C3 Mdga1 ACD Bio Cat# 546411, 546411-C2 Nlgn2 ACD Bio Cat# 406681 Negative Control ACD Bio Cat# 320871 Positive Control ACD Bio Cat# 320881 probe diluent ACD Bio Cat# 300041 Slc17a7 ACD Bio Cat# 416631-C2, 416631, 416631-C3 Cdh13 ACD Bio Cat# 443251-C3 Chrm2 ACD Bio Cat# 495311-C2 (Continued on next page) e1 Cell 185, 311–327.e1–e11, January 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deptor ACD Bio Cat# 481561 - C3 Gad1 ACD Bio Cat# 400951-C2 Trpc6 ACD Bio Cat# 442951 Tshz2 ACD Bio Cat# 431061-C1 Bacterial and virus strains pGP-AAV-syn-jGCaMP7f-WPRE Addgene 104488-PHPeB Critical commercial assays Multiplex RNAscope v2 Cat# 323110 Chromium Single Cell Library and Gel Bead Kit v2 10X Genomics Cat# 120237 Chromium Single Cell A Chip Kit 10X Genomics Cat# 1000009 Deposited data Raw single-nucleus sequencing data NCBI GEO GEO: GSE190940 Visualized atlas Single Cell Portal Single Cell Portal SCP1664 Tuning kernels and SNR values for all neurons in 2P imaging Figshare https://figshare.com/articles/dataset/Vision- dependent_specification_of_cell_types_and_ function_in_the_developing_cortex/16992544 Experimental models: Organisms/strains Mouse: C57BL/6J JAX 664 Mouse: Igsf9b Gene trap in C57BL/6J background Gifted by the Krueger-Burg lab Gifted by the Krueger-Burg lab Software and algorithms Cell Ranger v2.1.0 10X Genomics www.support.10xgenomics.com/single-cell- gene-expression/software/overview/welcome FIJI (ImageJ) https://imagej.nih.gov/ij Zen Zeiss www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Linlab2 Scientifica https://www.scientifica.uk.com/products/ scientifica-linlab-2 MATLAB Mathworks mathworks.com Processing3 Processing Processing.org Suite2P https://suite2p.readthedocs.io/en/latest/ Cell Profiler v3.1.9 Broad Institute https://cellprofiler.org/ R R version 4.0.2 www.r-project.org/ Seurat 3.2.2 Stuart et al., 2019 https://github.com/satijalab/seurat Python 3.7 Anaconda3 www.anaconda.com SCANPY Wolf et al., 2018 https://scanpy.readthedocs.io/en/stable/ Scrublet Wolock et al., 2019 https://github.com/swolock/scrublet XGBoost Chen and Guestrin, 2016 https://xgboost.readthedocs.io/en/latest/ Harmony Korsunsky et al., 2019 https://github.com/immunogenomics/harmony Other LSM 880 Zeiss Resonant-Galvo scanning 2-photon microscope Neurolabware http://neurolabware.com/ Nanoject III Drummond Scientific https://www.drummondsci.com/microinjection/ nanoject-iii-programmable-nanoliter-injector/ Scientifica PatchStar Micromanipulator Scientifica https://www.scientifica.uk.com/products/ scientifica-patchstar-micromanipulator Chromium Controller 10X Genomics https://www.10xgenomics.com/instruments/ chromium-controller Leica CM1950 cryostat Leica https://www2.leicabiosystems.com/ Peel-A-Way Disposable Embedding Mold Polysciences Cat# 18646A-1 Black Rubberized Fabric Thorlabs Cat# BK5 ll Cell 185, 311–327.e1–e11, January 20, 2022 e2 Article ll Article .. Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, S. Lawrence Zipursky (lzipursky@mednet.ucla.edu).

    Software:

    Article Title: Vision-dependent specification of cell types and function in the developing cortex.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies VGLUT1 guinea pig polyclonal Millipore Sigma Cat# AB5905; RRID:AB_2301751 GAD65 mouse monoclonal Millipore Sigma Cat# MAB3521R; RRID:AB_94905 VGLUT2 guinea pig polyclonal Synaptic Systems Cat# 135404; RRID:AB_887884 NLGN2 guinea pig polyclonal Synaptic Systems Cat# 129205; RRID:AB_2619815 GABRA1 rabbit polyclonal Synaptic Systems Cat# 224203; RRID:AB_2232180 GABRG2 guinea pig polyclonal Synaptic Systems Cat# 224004; RRID:AB_10594245 VGAT rabbit polyclonal Synaptic Systems Cat# 131002; RRID:AB_887871 PSD95 rabbit polyclonal Thermo Fisher Cat# 516900; RRID:AB_2533914 SSCAM rabbit polyclonal Sigma Aldrich Cat# 2441; RRID:AB_477175 Goat anti-guinea pig polyclonal 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-mouse polyclonal 488 Invitrogen Cat# A11029; RRID:AB_138404 Goat anti-guinea pig 647 Life Technologies Cat# A21450; RRID:AB_141882 Goat anti-guinea pig 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-rabbit 488 Life Technologies Cat# A11008; RRID:AB_143165 Goat anti-mouse 568 Invitrogen Cat# A11031; RRID:AB_144696 Goat anti-rabbit 647 Invitrogen Cat# A21244; RRID:AB_2535812 Goat anti-rabbit 568 Invitrogen Cat# A11011; RRID:AB_143157 Chemicals, peptides, and recombinant proteins Prolong Gold Thermo Fisher Scientific Cat# P36930 Normal Goat Serum Sigma-Aldrich Cat# G6767 Paraformaldehyde Electron Microscopy Services Cat# 15714 2-methylbutane Sigma-Aldrich Cat# 277258 10X PBS Invitrogen Cat# AM9625 Tissue-Tek OCT compound, Sakura VMR Cat# 4583 RNAse inhibitor New England Biolabs Cat# M0314L 50x protease inhibitor Sigma-Aldrich Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 RNA later Thermo Fisher Scientific Cat# AM7020 Hibernate A minus calcium BrainBits Cat# HACA BSA (Bovine Serum Albumin) Sigma-Aldrich Cat# B6917 Ultrapure Dnase/Rnase Free distilled water Thermo Fisher Scientific Cat# 10-977-023 Ultrapure DEPC-treated water Thermo Fisher Scientific Cat# 10813012 Sucrose, Rnase, Dnase free Thermo Fisher Scientific Cat# AC419762500 D-Mannitol MilliporeSigma Cat# M9546-250G Igsf9b ACD Bio Cat# 832171-C3 Mdga1 ACD Bio Cat# 546411, 546411-C2 Nlgn2 ACD Bio Cat# 406681 Negative Control ACD Bio Cat# 320871 Positive Control ACD Bio Cat# 320881 probe diluent ACD Bio Cat# 300041 Slc17a7 ACD Bio Cat# 416631-C2, 416631, 416631-C3 Cdh13 ACD Bio Cat# 443251-C3 Chrm2 ACD Bio Cat# 495311-C2 (Continued on next page) e1 Cell 185, 311–327.e1–e11, January 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deptor ACD Bio Cat# 481561 - C3 Gad1 ACD Bio Cat# 400951-C2 Trpc6 ACD Bio Cat# 442951 Tshz2 ACD Bio Cat# 431061-C1 Bacterial and virus strains pGP-AAV-syn-jGCaMP7f-WPRE Addgene 104488-PHPeB Critical commercial assays Multiplex RNAscope v2 Cat# 323110 Chromium Single Cell Library and Gel Bead Kit v2 10X Genomics Cat# 120237 Chromium Single Cell A Chip Kit 10X Genomics Cat# 1000009 Deposited data Raw single-nucleus sequencing data NCBI GEO GEO: GSE190940 Visualized atlas Single Cell Portal Single Cell Portal SCP1664 Tuning kernels and SNR values for all neurons in 2P imaging Figshare https://figshare.com/articles/dataset/Vision- dependent_specification_of_cell_types_and_ function_in_the_developing_cortex/16992544 Experimental models: Organisms/strains Mouse: C57BL/6J JAX 664 Mouse: Igsf9b Gene trap in C57BL/6J background Gifted by the Krueger-Burg lab Gifted by the Krueger-Burg lab Software and algorithms Cell Ranger v2.1.0 10X Genomics www.support.10xgenomics.com/single-cell- gene-expression/software/overview/welcome FIJI (ImageJ) https://imagej.nih.gov/ij Zen Zeiss www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Linlab2 Scientifica https://www.scientifica.uk.com/products/ scientifica-linlab-2 MATLAB Mathworks mathworks.com Processing3 Processing Processing.org Suite2P https://suite2p.readthedocs.io/en/latest/ Cell Profiler v3.1.9 Broad Institute https://cellprofiler.org/ R R version 4.0.2 www.r-project.org/ Seurat 3.2.2 Stuart et al., 2019 https://github.com/satijalab/seurat Python 3.7 Anaconda3 www.anaconda.com SCANPY Wolf et al., 2018 https://scanpy.readthedocs.io/en/stable/ Scrublet Wolock et al., 2019 https://github.com/swolock/scrublet XGBoost Chen and Guestrin, 2016 https://xgboost.readthedocs.io/en/latest/ Harmony Korsunsky et al., 2019 https://github.com/immunogenomics/harmony Other LSM 880 Zeiss Resonant-Galvo scanning 2-photon microscope Neurolabware http://neurolabware.com/ Nanoject III Drummond Scientific https://www.drummondsci.com/microinjection/ nanoject-iii-programmable-nanoliter-injector/ Scientifica PatchStar Micromanipulator Scientifica https://www.scientifica.uk.com/products/ scientifica-patchstar-micromanipulator Chromium Controller 10X Genomics https://www.10xgenomics.com/instruments/ chromium-controller Leica CM1950 cryostat Leica https://www2.leicabiosystems.com/ Peel-A-Way Disposable Embedding Mold Polysciences Cat# 18646A-1 Black Rubberized Fabric Thorlabs Cat# BK5 ll Cell 185, 311–327.e1–e11, January 20, 2022 e2 Article ll Article .. Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, S. Lawrence Zipursky (lzipursky@mednet.ucla.edu).

    Microscopy:

    Article Title: Vision-dependent specification of cell types and function in the developing cortex.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies VGLUT1 guinea pig polyclonal Millipore Sigma Cat# AB5905; RRID:AB_2301751 GAD65 mouse monoclonal Millipore Sigma Cat# MAB3521R; RRID:AB_94905 VGLUT2 guinea pig polyclonal Synaptic Systems Cat# 135404; RRID:AB_887884 NLGN2 guinea pig polyclonal Synaptic Systems Cat# 129205; RRID:AB_2619815 GABRA1 rabbit polyclonal Synaptic Systems Cat# 224203; RRID:AB_2232180 GABRG2 guinea pig polyclonal Synaptic Systems Cat# 224004; RRID:AB_10594245 VGAT rabbit polyclonal Synaptic Systems Cat# 131002; RRID:AB_887871 PSD95 rabbit polyclonal Thermo Fisher Cat# 516900; RRID:AB_2533914 SSCAM rabbit polyclonal Sigma Aldrich Cat# 2441; RRID:AB_477175 Goat anti-guinea pig polyclonal 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-mouse polyclonal 488 Invitrogen Cat# A11029; RRID:AB_138404 Goat anti-guinea pig 647 Life Technologies Cat# A21450; RRID:AB_141882 Goat anti-guinea pig 568 Invitrogen Cat# A11075; RRID:AB_141954 Goat anti-rabbit 488 Life Technologies Cat# A11008; RRID:AB_143165 Goat anti-mouse 568 Invitrogen Cat# A11031; RRID:AB_144696 Goat anti-rabbit 647 Invitrogen Cat# A21244; RRID:AB_2535812 Goat anti-rabbit 568 Invitrogen Cat# A11011; RRID:AB_143157 Chemicals, peptides, and recombinant proteins Prolong Gold Thermo Fisher Scientific Cat# P36930 Normal Goat Serum Sigma-Aldrich Cat# G6767 Paraformaldehyde Electron Microscopy Services Cat# 15714 2-methylbutane Sigma-Aldrich Cat# 277258 10X PBS Invitrogen Cat# AM9625 Tissue-Tek OCT compound, Sakura VMR Cat# 4583 RNAse inhibitor New England Biolabs Cat# M0314L 50x protease inhibitor Sigma-Aldrich Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 RNA later Thermo Fisher Scientific Cat# AM7020 Hibernate A minus calcium BrainBits Cat# HACA BSA (Bovine Serum Albumin) Sigma-Aldrich Cat# B6917 Ultrapure Dnase/Rnase Free distilled water Thermo Fisher Scientific Cat# 10-977-023 Ultrapure DEPC-treated water Thermo Fisher Scientific Cat# 10813012 Sucrose, Rnase, Dnase free Thermo Fisher Scientific Cat# AC419762500 D-Mannitol MilliporeSigma Cat# M9546-250G Igsf9b ACD Bio Cat# 832171-C3 Mdga1 ACD Bio Cat# 546411, 546411-C2 Nlgn2 ACD Bio Cat# 406681 Negative Control ACD Bio Cat# 320871 Positive Control ACD Bio Cat# 320881 probe diluent ACD Bio Cat# 300041 Slc17a7 ACD Bio Cat# 416631-C2, 416631, 416631-C3 Cdh13 ACD Bio Cat# 443251-C3 Chrm2 ACD Bio Cat# 495311-C2 (Continued on next page) e1 Cell 185, 311–327.e1–e11, January 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deptor ACD Bio Cat# 481561 - C3 Gad1 ACD Bio Cat# 400951-C2 Trpc6 ACD Bio Cat# 442951 Tshz2 ACD Bio Cat# 431061-C1 Bacterial and virus strains pGP-AAV-syn-jGCaMP7f-WPRE Addgene 104488-PHPeB Critical commercial assays Multiplex RNAscope v2 Cat# 323110 Chromium Single Cell Library and Gel Bead Kit v2 10X Genomics Cat# 120237 Chromium Single Cell A Chip Kit 10X Genomics Cat# 1000009 Deposited data Raw single-nucleus sequencing data NCBI GEO GEO: GSE190940 Visualized atlas Single Cell Portal Single Cell Portal SCP1664 Tuning kernels and SNR values for all neurons in 2P imaging Figshare https://figshare.com/articles/dataset/Vision- dependent_specification_of_cell_types_and_ function_in_the_developing_cortex/16992544 Experimental models: Organisms/strains Mouse: C57BL/6J JAX 664 Mouse: Igsf9b Gene trap in C57BL/6J background Gifted by the Krueger-Burg lab Gifted by the Krueger-Burg lab Software and algorithms Cell Ranger v2.1.0 10X Genomics www.support.10xgenomics.com/single-cell- gene-expression/software/overview/welcome FIJI (ImageJ) https://imagej.nih.gov/ij Zen Zeiss www.zeiss.com/microscopy/int/products/ microscope-software/zen.html Linlab2 Scientifica https://www.scientifica.uk.com/products/ scientifica-linlab-2 MATLAB Mathworks mathworks.com Processing3 Processing Processing.org Suite2P https://suite2p.readthedocs.io/en/latest/ Cell Profiler v3.1.9 Broad Institute https://cellprofiler.org/ R R version 4.0.2 www.r-project.org/ Seurat 3.2.2 Stuart et al., 2019 https://github.com/satijalab/seurat Python 3.7 Anaconda3 www.anaconda.com SCANPY Wolf et al., 2018 https://scanpy.readthedocs.io/en/stable/ Scrublet Wolock et al., 2019 https://github.com/swolock/scrublet XGBoost Chen and Guestrin, 2016 https://xgboost.readthedocs.io/en/latest/ Harmony Korsunsky et al., 2019 https://github.com/immunogenomics/harmony Other LSM 880 Zeiss Resonant-Galvo scanning 2-photon microscope Neurolabware http://neurolabware.com/ Nanoject III Drummond Scientific https://www.drummondsci.com/microinjection/ nanoject-iii-programmable-nanoliter-injector/ Scientifica PatchStar Micromanipulator Scientifica https://www.scientifica.uk.com/products/ scientifica-patchstar-micromanipulator Chromium Controller 10X Genomics https://www.10xgenomics.com/instruments/ chromium-controller Leica CM1950 cryostat Leica https://www2.leicabiosystems.com/ Peel-A-Way Disposable Embedding Mold Polysciences Cat# 18646A-1 Black Rubberized Fabric Thorlabs Cat# BK5 ll Cell 185, 311–327.e1–e11, January 20, 2022 e2 Article ll Article .. Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contact, S. Lawrence Zipursky (lzipursky@mednet.ucla.edu).



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    3d image processing software (simpleware scanip, version m-2021.06 - by Bioz Stars, 2026-10
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    synopysis simpleware scanip image processing software  (Simpleware Ltd)
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    Simpleware Ltd synopysis simpleware scanip image processing software
    A pathway describing the process used to manually segment the VS tumors <t>from</t> <t>MRI</t> images using the imaging processing software Simpleware <t>ScanIP.</t>
    Synopysis Simpleware Scanip Image Processing Software, supplied by Simpleware Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/image-processing+software+scanip/synopsys+simpleware/pmc10905807-35-15-2
    Average 90 stars, based on 1 article reviews
    synopysis simpleware scanip image processing software - by Bioz Stars, 2026-10
    90/100 stars
    		  Buy from Supplier
    image processing software scanip  (Simpleware Ltd)
    90
    Simpleware Ltd image processing software scanip
    A pathway describing the process used to manually segment the VS tumors <t>from</t> <t>MRI</t> images using the imaging processing software Simpleware <t>ScanIP.</t>
    Image Processing Software Scanip, supplied by Simpleware Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/image-processing+software+scanip/scanip+software/pm38247900-60-6-10
    Average 90 stars, based on 1 article reviews
    image processing software scanip - by Bioz Stars, 2026-10
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    		  Buy from Supplier

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    A pathway describing the process used to manually segment the VS tumors from MRI images using the imaging processing software Simpleware ScanIP.

    Journal: Scientific Reports

    Article Title: The development of an artificial intelligence auto-segmentation tool for 3D volumetric analysis of vestibular schwannomas

    doi: 10.1038/s41598-025-88589-x

    Figure Lengend Snippet: A pathway describing the process used to manually segment the VS tumors from MRI images using the imaging processing software Simpleware ScanIP.

    Article Snippet: 3D tumor masks were created for vestibular schwannomas (unilateral or bilateral) as follows (Fig. ): Fig. 2 A pathway describing the process used to manually segment the VS tumors from MRI images using the imaging processing software Simpleware ScanIP.

    Techniques: Imaging, Software