modified constrained non-negative matrix factorization scripts cnmf_e Search Results


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constrained non negative matrix factorization  (Inscopix Inc)
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Inscopix Inc constrained non negative matrix factorization
( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. <t>Constrained</t> <t>non-negative</t> matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).
Constrained Non Negative Matrix Factorization, supplied by Inscopix Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. <t>Constrained</t> <t>non-negative</t> matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).
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( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. <t>Constrained</t> <t>non-negative</t> matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).
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a 31572 bacterial  (Addgene inc)
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Addgene inc a 31572 bacterial
( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. <t>Constrained</t> <t>non-negative</t> matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).
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av 1 pv2819 aav1 ef1α dio gcamp6s p2a nls dtomato addgene  (Addgene inc)
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paper addgene id 110134 paav cba do fas gcamp6s  (Addgene inc)
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A. AAVs expressing Cre-On jRCaMP1b and Cre-Off <t>GCaMP6s</t> were injected into the DLS to assess direct (dSPN, red) and indirect (iSPN, green) pathway activity via multicolor photometry (see Methods). Top, sagittal schematic of injection site. Middle and bottom, histological verification of jRCaMP1b (dSPN, red) and GCaMP6s (iSPN, green) expression (sagittal sections, SNr = substantia nigra pars reticulata, GP = globus pallidus). Scale bar, 1 mm.
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aav1  (Addgene inc)
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A. AAVs expressing Cre-On jRCaMP1b and Cre-Off <t>GCaMP6s</t> were injected into the DLS to assess direct (dSPN, red) and indirect (iSPN, green) pathway activity via multicolor photometry (see Methods). Top, sagittal schematic of injection site. Middle and bottom, histological verification of jRCaMP1b (dSPN, red) and GCaMP6s (iSPN, green) expression (sagittal sections, SNr = substantia nigra pars reticulata, GP = globus pallidus). Scale bar, 1 mm.
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A. AAVs expressing Cre-On jRCaMP1b and Cre-Off <t>GCaMP6s</t> were injected into the DLS to assess direct (dSPN, red) and indirect (iSPN, green) pathway activity via multicolor photometry (see Methods). Top, sagittal schematic of injection site. Middle and bottom, histological verification of jRCaMP1b (dSPN, red) and GCaMP6s (iSPN, green) expression (sagittal sections, SNr = substantia nigra pars reticulata, GP = globus pallidus). Scale bar, 1 mm.
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A. AAVs expressing Cre-On jRCaMP1b and Cre-Off <t>GCaMP6s</t> were injected into the DLS to assess direct (dSPN, red) and indirect (iSPN, green) pathway activity via multicolor photometry (see Methods). Top, sagittal schematic of injection site. Middle and bottom, histological verification of jRCaMP1b (dSPN, red) and GCaMP6s (iSPN, green) expression (sagittal sections, SNr = substantia nigra pars reticulata, GP = globus pallidus). Scale bar, 1 mm.
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A. AAVs expressing Cre-On jRCaMP1b and Cre-Off <t>GCaMP6s</t> were injected into the DLS to assess direct (dSPN, red) and indirect (iSPN, green) pathway activity via multicolor photometry (see Methods). Top, sagittal schematic of injection site. Middle and bottom, histological verification of jRCaMP1b (dSPN, red) and GCaMP6s (iSPN, green) expression (sagittal sections, SNr = substantia nigra pars reticulata, GP = globus pallidus). Scale bar, 1 mm.
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Image Search Results


( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Article Snippet: We extracted spatial and temporal components of neuronal activity from miniscope videos using constrained non-negative matrix factorization for endoscopic data (CNMF-E) implemented through the Inscopix Data Processing Software.

Techniques: Injection, Imaging, Generated, Activity Assay

Key Resources Table

Journal: Cell

Article Title: The striatum organizes 3D behavior via moment-to-moment action selection

doi: 10.1016/j.cell.2018.04.019

Figure Lengend Snippet: Key Resources Table

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Chicken Anti-GFAP abcam Cat# ab4674 Alexa Fluor 488, Donkey Anti-Chicken IgY Jackson Laboratory Cat# 703-545-155 Rabbit Anti-NeuN abcam Cat# ab104225 Alex Fluor 555, Donkey Anti-Rabbit IgG Thermo-Fisher Cat# A-31572 Bacterial and Virus Strains AAV9-CBA-do(Fas)-GCaMP6s UNC Vector Core N/A AAV9-CBA-DIO-jRCaMP1b UNC Vector Core N/A AAV1.Syn.Flex.GCaMP6f.WPRE.SV40 Penn Vector Core Cat# AV-1-PV2819 AAV1.EF1α.DIO.GCaMP6s.P2A.NLS.dTomato Addgene Cat# 51082 Chemicals, Peptides, and Recombinant Proteins N-Methyl-D-aspartic acid Sigma-Aldrich Cat# M3262-250MG Experimental Models: Organisms/Strains Mouse: B6.FVB(Cg)-Tg(Drd1-cre)EY262Gsat/Mmucd MMRRC-UCD MMRRC Stock# 030989-UCD Mouse: B6.FVB(Cg)-Tg(Adora2a-cre) KG139Gsat/Mmucd MMRRC-UCD MMRRC Stock# 036158-UCD Mouse: C57BL/6J Jackson Laboratory Jax stock #000664 Mouse: B6;129S-Pdyn tm1.1(cre)Mjkr /LowlJ Jackson Laboratory Jax stock #027958 Recombinant DNA pAAV-CBA-DIO-jRCaMP1b This paper Addgene ID 110134 pAAV-CBA-do(Fas)-GCaMP6s This paper Addgene ID 110135 Software and Algorithms MoSeq ( Wiltschko et al., 2015 ) N/A MATLAB The MathWorks https://www.mathworks.com/products/matlab.html Constrained Non-negative Matrix Factorization for microendoscope data (CNMF-E) ( Zhou et al., 2018 ) N/A Mosaic version 1.2.0 Inscopix https://www.inscopix.com Intan Recording System Software Intan Technologies http://intantech.com/downloads.html Other Kinect for Xbox One (Kinect 2) Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect Xbox One S Kinect Adapter Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect/kinect-adapter Shallow tank US Plastic Cat# 14317 Open in a separate window Key Resources Table

Techniques: Plasmid Preparation, Recombinant, Software

A. AAVs expressing Cre-On jRCaMP1b and Cre-Off GCaMP6s were injected into the DLS to assess direct (dSPN, red) and indirect (iSPN, green) pathway activity via multicolor photometry (see Methods). Top, sagittal schematic of injection site. Middle and bottom, histological verification of jRCaMP1b (dSPN, red) and GCaMP6s (iSPN, green) expression (sagittal sections, SNr = substantia nigra pars reticulata, GP = globus pallidus). Scale bar, 1 mm.

Journal: Cell

Article Title: The striatum organizes 3D behavior via moment-to-moment action selection

doi: 10.1016/j.cell.2018.04.019

Figure Lengend Snippet: A. AAVs expressing Cre-On jRCaMP1b and Cre-Off GCaMP6s were injected into the DLS to assess direct (dSPN, red) and indirect (iSPN, green) pathway activity via multicolor photometry (see Methods). Top, sagittal schematic of injection site. Middle and bottom, histological verification of jRCaMP1b (dSPN, red) and GCaMP6s (iSPN, green) expression (sagittal sections, SNr = substantia nigra pars reticulata, GP = globus pallidus). Scale bar, 1 mm.

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Chicken Anti-GFAP abcam Cat# ab4674 Alexa Fluor 488, Donkey Anti-Chicken IgY Jackson Laboratory Cat# 703-545-155 Rabbit Anti-NeuN abcam Cat# ab104225 Alex Fluor 555, Donkey Anti-Rabbit IgG Thermo-Fisher Cat# A-31572 Bacterial and Virus Strains AAV9-CBA-do(Fas)-GCaMP6s UNC Vector Core N/A AAV9-CBA-DIO-jRCaMP1b UNC Vector Core N/A AAV1.Syn.Flex.GCaMP6f.WPRE.SV40 Penn Vector Core Cat# AV-1-PV2819 AAV1.EF1α.DIO.GCaMP6s.P2A.NLS.dTomato Addgene Cat# 51082 Chemicals, Peptides, and Recombinant Proteins N-Methyl-D-aspartic acid Sigma-Aldrich Cat# M3262-250MG Experimental Models: Organisms/Strains Mouse: B6.FVB(Cg)-Tg(Drd1-cre)EY262Gsat/Mmucd MMRRC-UCD MMRRC Stock# 030989-UCD Mouse: B6.FVB(Cg)-Tg(Adora2a-cre) KG139Gsat/Mmucd MMRRC-UCD MMRRC Stock# 036158-UCD Mouse: C57BL/6J Jackson Laboratory Jax stock #000664 Mouse: B6;129S-Pdyn tm1.1(cre)Mjkr /LowlJ Jackson Laboratory Jax stock #027958 Recombinant DNA pAAV-CBA-DIO-jRCaMP1b This paper Addgene ID 110134 pAAV-CBA-do(Fas)-GCaMP6s This paper Addgene ID 110135 Software and Algorithms MoSeq ( Wiltschko et al., 2015 ) N/A MATLAB The MathWorks https://www.mathworks.com/products/matlab.html Constrained Non-negative Matrix Factorization for microendoscope data (CNMF-E) ( Zhou et al., 2018 ) N/A Mosaic version 1.2.0 Inscopix https://www.inscopix.com Intan Recording System Software Intan Technologies http://intantech.com/downloads.html Other Kinect for Xbox One (Kinect 2) Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect Xbox One S Kinect Adapter Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect/kinect-adapter Shallow tank US Plastic Cat# 14317 Open in a separate window Key Resources Table

Techniques: Expressing, Injection, Activity Assay

Key Resources Table

Journal: Cell

Article Title: The striatum organizes 3D behavior via moment-to-moment action selection

doi: 10.1016/j.cell.2018.04.019

Figure Lengend Snippet: Key Resources Table

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Chicken Anti-GFAP abcam Cat# ab4674 Alexa Fluor 488, Donkey Anti-Chicken IgY Jackson Laboratory Cat# 703-545-155 Rabbit Anti-NeuN abcam Cat# ab104225 Alex Fluor 555, Donkey Anti-Rabbit IgG Thermo-Fisher Cat# A-31572 Bacterial and Virus Strains AAV9-CBA-do(Fas)-GCaMP6s UNC Vector Core N/A AAV9-CBA-DIO-jRCaMP1b UNC Vector Core N/A AAV1.Syn.Flex.GCaMP6f.WPRE.SV40 Penn Vector Core Cat# AV-1-PV2819 AAV1.EF1α.DIO.GCaMP6s.P2A.NLS.dTomato Addgene Cat# 51082 Chemicals, Peptides, and Recombinant Proteins N-Methyl-D-aspartic acid Sigma-Aldrich Cat# M3262-250MG Experimental Models: Organisms/Strains Mouse: B6.FVB(Cg)-Tg(Drd1-cre)EY262Gsat/Mmucd MMRRC-UCD MMRRC Stock# 030989-UCD Mouse: B6.FVB(Cg)-Tg(Adora2a-cre) KG139Gsat/Mmucd MMRRC-UCD MMRRC Stock# 036158-UCD Mouse: C57BL/6J Jackson Laboratory Jax stock #000664 Mouse: B6;129S-Pdyn tm1.1(cre)Mjkr /LowlJ Jackson Laboratory Jax stock #027958 Recombinant DNA pAAV-CBA-DIO-jRCaMP1b This paper Addgene ID 110134 pAAV-CBA-do(Fas)-GCaMP6s This paper Addgene ID 110135 Software and Algorithms MoSeq ( Wiltschko et al., 2015 ) N/A MATLAB The MathWorks https://www.mathworks.com/products/matlab.html Constrained Non-negative Matrix Factorization for microendoscope data (CNMF-E) ( Zhou et al., 2018 ) N/A Mosaic version 1.2.0 Inscopix https://www.inscopix.com Intan Recording System Software Intan Technologies http://intantech.com/downloads.html Other Kinect for Xbox One (Kinect 2) Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect Xbox One S Kinect Adapter Microsoft https://www.xbox.com/en-US/xboxone/accessories/kinect/kinect-adapter Shallow tank US Plastic Cat# 14317 Open in a separate window Key Resources Table

Techniques: Plasmid Preparation, Recombinant, Software