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kernel csd toolbox  (MathWorks Inc)


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    MathWorks Inc kernel csd toolbox
    a The UOA used in the in vivo experiments inserted in macaque V1. b Same field of view as in ( a ) shown under fluorescent illumination to reveal expression of the red fluorescent protein tdTomato (arrow). c Preparation for recording electrophysiological responses to photostimulation. A 24 channel linear electrode array (LEA) was inserted next to the UOA (guide tube protecting array marked “LEA”) slightly angled laterally (towards the UOA) and posteriorly. Here the UOA is partially covered with a piece of Gelfoam. d <t>Current</t> <t>Source</t> <t>Density</t> analysis <t>(CSD;</t> Left) and MUA (Right) signals recorded through the depth of V1 in LEA-P2 in response to phasic UOA photostimulation (pulse parameters: 100 ms pulse duration, 5 Hz, 0.82 mW/mm 2 ; pulse periods denoted as blue bars above MUA plot). Here, all 100 needle-aligned µLED sites (“whole µLED array” condition) were activated simultaneously. CSD responses to each 100 ms pulse were zero-aligned ( n = 170 pulses), while MUA is shown for the full 5 Hz pulse train ( n = 34 trials). The dashed lines in the CSD panel demarcate the borders of layer 4 C (L4C); the gray shaded region in the MUA panel delimits the extent of L4C. e Same as in d , but following surface photostimulation of V1 via a laser-coupled optical fiber with pulse parameters of 10 ms, 5 Hz, 2.2 mW/mm 2 ( n = 160 pulses, 32 trials). f – i Top: relative cortical depth of each contact on LEA-P2 (black dot in the insets) is plotted versus the relative response (% firing rate increase over baseline) to UOA stimulation for different 450 nm µLED illumination patterns (top insets) ( n = 125–205 pulses per condition). Different colored traces are data for different photostimulation intensities (expressed as voltage or percent of max intensity used). Gray area: extent of L4C; dashed lines: approximate location of the L4A/4B (upper) and L5/L6 (lower) borders. In all panels, error bars represent standard error of the mean. Bottom: PSTHs with and without µLED activation are shown for the same contact on the LEA in L4C (marked by the black circle in the graphs above) across conditions. Dashed line in the PSTH: pulse periods. In all panels, error bars represent standard error of the mean.
    Kernel Csd Toolbox, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "An optrode array for spatiotemporally-precise large-scale optogenetic stimulation of deep cortical layers in non-human primates"

    Article Title: An optrode array for spatiotemporally-precise large-scale optogenetic stimulation of deep cortical layers in non-human primates

    Journal: Communications Biology

    doi: 10.1038/s42003-024-05984-2

    a The UOA used in the in vivo experiments inserted in macaque V1. b Same field of view as in ( a ) shown under fluorescent illumination to reveal expression of the red fluorescent protein tdTomato (arrow). c Preparation for recording electrophysiological responses to photostimulation. A 24 channel linear electrode array (LEA) was inserted next to the UOA (guide tube protecting array marked “LEA”) slightly angled laterally (towards the UOA) and posteriorly. Here the UOA is partially covered with a piece of Gelfoam. d Current Source Density analysis (CSD; Left) and MUA (Right) signals recorded through the depth of V1 in LEA-P2 in response to phasic UOA photostimulation (pulse parameters: 100 ms pulse duration, 5 Hz, 0.82 mW/mm 2 ; pulse periods denoted as blue bars above MUA plot). Here, all 100 needle-aligned µLED sites (“whole µLED array” condition) were activated simultaneously. CSD responses to each 100 ms pulse were zero-aligned ( n = 170 pulses), while MUA is shown for the full 5 Hz pulse train ( n = 34 trials). The dashed lines in the CSD panel demarcate the borders of layer 4 C (L4C); the gray shaded region in the MUA panel delimits the extent of L4C. e Same as in d , but following surface photostimulation of V1 via a laser-coupled optical fiber with pulse parameters of 10 ms, 5 Hz, 2.2 mW/mm 2 ( n = 160 pulses, 32 trials). f – i Top: relative cortical depth of each contact on LEA-P2 (black dot in the insets) is plotted versus the relative response (% firing rate increase over baseline) to UOA stimulation for different 450 nm µLED illumination patterns (top insets) ( n = 125–205 pulses per condition). Different colored traces are data for different photostimulation intensities (expressed as voltage or percent of max intensity used). Gray area: extent of L4C; dashed lines: approximate location of the L4A/4B (upper) and L5/L6 (lower) borders. In all panels, error bars represent standard error of the mean. Bottom: PSTHs with and without µLED activation are shown for the same contact on the LEA in L4C (marked by the black circle in the graphs above) across conditions. Dashed line in the PSTH: pulse periods. In all panels, error bars represent standard error of the mean.
    Figure Legend Snippet: a The UOA used in the in vivo experiments inserted in macaque V1. b Same field of view as in ( a ) shown under fluorescent illumination to reveal expression of the red fluorescent protein tdTomato (arrow). c Preparation for recording electrophysiological responses to photostimulation. A 24 channel linear electrode array (LEA) was inserted next to the UOA (guide tube protecting array marked “LEA”) slightly angled laterally (towards the UOA) and posteriorly. Here the UOA is partially covered with a piece of Gelfoam. d Current Source Density analysis (CSD; Left) and MUA (Right) signals recorded through the depth of V1 in LEA-P2 in response to phasic UOA photostimulation (pulse parameters: 100 ms pulse duration, 5 Hz, 0.82 mW/mm 2 ; pulse periods denoted as blue bars above MUA plot). Here, all 100 needle-aligned µLED sites (“whole µLED array” condition) were activated simultaneously. CSD responses to each 100 ms pulse were zero-aligned ( n = 170 pulses), while MUA is shown for the full 5 Hz pulse train ( n = 34 trials). The dashed lines in the CSD panel demarcate the borders of layer 4 C (L4C); the gray shaded region in the MUA panel delimits the extent of L4C. e Same as in d , but following surface photostimulation of V1 via a laser-coupled optical fiber with pulse parameters of 10 ms, 5 Hz, 2.2 mW/mm 2 ( n = 160 pulses, 32 trials). f – i Top: relative cortical depth of each contact on LEA-P2 (black dot in the insets) is plotted versus the relative response (% firing rate increase over baseline) to UOA stimulation for different 450 nm µLED illumination patterns (top insets) ( n = 125–205 pulses per condition). Different colored traces are data for different photostimulation intensities (expressed as voltage or percent of max intensity used). Gray area: extent of L4C; dashed lines: approximate location of the L4A/4B (upper) and L5/L6 (lower) borders. In all panels, error bars represent standard error of the mean. Bottom: PSTHs with and without µLED activation are shown for the same contact on the LEA in L4C (marked by the black circle in the graphs above) across conditions. Dashed line in the PSTH: pulse periods. In all panels, error bars represent standard error of the mean.

    Techniques Used: In Vivo, Expressing, Activation Assay



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    a The UOA used in the in vivo experiments inserted in macaque V1. b Same field of view as in ( a ) shown under fluorescent illumination to reveal expression of the red fluorescent protein tdTomato (arrow). c Preparation for recording electrophysiological responses to photostimulation. A 24 channel linear electrode array (LEA) was inserted next to the UOA (guide tube protecting array marked “LEA”) slightly angled laterally (towards the UOA) and posteriorly. Here the UOA is partially covered with a piece of Gelfoam. d <t>Current</t> <t>Source</t> <t>Density</t> analysis <t>(CSD;</t> Left) and MUA (Right) signals recorded through the depth of V1 in LEA-P2 in response to phasic UOA photostimulation (pulse parameters: 100 ms pulse duration, 5 Hz, 0.82 mW/mm 2 ; pulse periods denoted as blue bars above MUA plot). Here, all 100 needle-aligned µLED sites (“whole µLED array” condition) were activated simultaneously. CSD responses to each 100 ms pulse were zero-aligned ( n = 170 pulses), while MUA is shown for the full 5 Hz pulse train ( n = 34 trials). The dashed lines in the CSD panel demarcate the borders of layer 4 C (L4C); the gray shaded region in the MUA panel delimits the extent of L4C. e Same as in d , but following surface photostimulation of V1 via a laser-coupled optical fiber with pulse parameters of 10 ms, 5 Hz, 2.2 mW/mm 2 ( n = 160 pulses, 32 trials). f – i Top: relative cortical depth of each contact on LEA-P2 (black dot in the insets) is plotted versus the relative response (% firing rate increase over baseline) to UOA stimulation for different 450 nm µLED illumination patterns (top insets) ( n = 125–205 pulses per condition). Different colored traces are data for different photostimulation intensities (expressed as voltage or percent of max intensity used). Gray area: extent of L4C; dashed lines: approximate location of the L4A/4B (upper) and L5/L6 (lower) borders. In all panels, error bars represent standard error of the mean. Bottom: PSTHs with and without µLED activation are shown for the same contact on the LEA in L4C (marked by the black circle in the graphs above) across conditions. Dashed line in the PSTH: pulse periods. In all panels, error bars represent standard error of the mean.
    Kernel Csd Toolbox, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    kernel csd toolbox kcsd_matlab  (MathWorks Inc)
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    MathWorks Inc kernel csd toolbox kcsd_matlab
    a The UOA used in the in vivo experiments inserted in macaque V1. b Same field of view as in ( a ) shown under fluorescent illumination to reveal expression of the red fluorescent protein tdTomato (arrow). c Preparation for recording electrophysiological responses to photostimulation. A 24 channel linear electrode array (LEA) was inserted next to the UOA (guide tube protecting array marked “LEA”) slightly angled laterally (towards the UOA) and posteriorly. Here the UOA is partially covered with a piece of Gelfoam. d <t>Current</t> <t>Source</t> <t>Density</t> analysis <t>(CSD;</t> Left) and MUA (Right) signals recorded through the depth of V1 in LEA-P2 in response to phasic UOA photostimulation (pulse parameters: 100 ms pulse duration, 5 Hz, 0.82 mW/mm 2 ; pulse periods denoted as blue bars above MUA plot). Here, all 100 needle-aligned µLED sites (“whole µLED array” condition) were activated simultaneously. CSD responses to each 100 ms pulse were zero-aligned ( n = 170 pulses), while MUA is shown for the full 5 Hz pulse train ( n = 34 trials). The dashed lines in the CSD panel demarcate the borders of layer 4 C (L4C); the gray shaded region in the MUA panel delimits the extent of L4C. e Same as in d , but following surface photostimulation of V1 via a laser-coupled optical fiber with pulse parameters of 10 ms, 5 Hz, 2.2 mW/mm 2 ( n = 160 pulses, 32 trials). f – i Top: relative cortical depth of each contact on LEA-P2 (black dot in the insets) is plotted versus the relative response (% firing rate increase over baseline) to UOA stimulation for different 450 nm µLED illumination patterns (top insets) ( n = 125–205 pulses per condition). Different colored traces are data for different photostimulation intensities (expressed as voltage or percent of max intensity used). Gray area: extent of L4C; dashed lines: approximate location of the L4A/4B (upper) and L5/L6 (lower) borders. In all panels, error bars represent standard error of the mean. Bottom: PSTHs with and without µLED activation are shown for the same contact on the LEA in L4C (marked by the black circle in the graphs above) across conditions. Dashed line in the PSTH: pulse periods. In all panels, error bars represent standard error of the mean.
    Kernel Csd Toolbox Kcsd Matlab, supplied by MathWorks Inc, 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/result/kernel csd toolbox kcsd_matlab/product/MathWorks Inc
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    a The UOA used in the in vivo experiments inserted in macaque V1. b Same field of view as in ( a ) shown under fluorescent illumination to reveal expression of the red fluorescent protein tdTomato (arrow). c Preparation for recording electrophysiological responses to photostimulation. A 24 channel linear electrode array (LEA) was inserted next to the UOA (guide tube protecting array marked “LEA”) slightly angled laterally (towards the UOA) and posteriorly. Here the UOA is partially covered with a piece of Gelfoam. d Current Source Density analysis (CSD; Left) and MUA (Right) signals recorded through the depth of V1 in LEA-P2 in response to phasic UOA photostimulation (pulse parameters: 100 ms pulse duration, 5 Hz, 0.82 mW/mm 2 ; pulse periods denoted as blue bars above MUA plot). Here, all 100 needle-aligned µLED sites (“whole µLED array” condition) were activated simultaneously. CSD responses to each 100 ms pulse were zero-aligned ( n = 170 pulses), while MUA is shown for the full 5 Hz pulse train ( n = 34 trials). The dashed lines in the CSD panel demarcate the borders of layer 4 C (L4C); the gray shaded region in the MUA panel delimits the extent of L4C. e Same as in d , but following surface photostimulation of V1 via a laser-coupled optical fiber with pulse parameters of 10 ms, 5 Hz, 2.2 mW/mm 2 ( n = 160 pulses, 32 trials). f – i Top: relative cortical depth of each contact on LEA-P2 (black dot in the insets) is plotted versus the relative response (% firing rate increase over baseline) to UOA stimulation for different 450 nm µLED illumination patterns (top insets) ( n = 125–205 pulses per condition). Different colored traces are data for different photostimulation intensities (expressed as voltage or percent of max intensity used). Gray area: extent of L4C; dashed lines: approximate location of the L4A/4B (upper) and L5/L6 (lower) borders. In all panels, error bars represent standard error of the mean. Bottom: PSTHs with and without µLED activation are shown for the same contact on the LEA in L4C (marked by the black circle in the graphs above) across conditions. Dashed line in the PSTH: pulse periods. In all panels, error bars represent standard error of the mean.

    Journal: Communications Biology

    Article Title: An optrode array for spatiotemporally-precise large-scale optogenetic stimulation of deep cortical layers in non-human primates

    doi: 10.1038/s42003-024-05984-2

    Figure Lengend Snippet: a The UOA used in the in vivo experiments inserted in macaque V1. b Same field of view as in ( a ) shown under fluorescent illumination to reveal expression of the red fluorescent protein tdTomato (arrow). c Preparation for recording electrophysiological responses to photostimulation. A 24 channel linear electrode array (LEA) was inserted next to the UOA (guide tube protecting array marked “LEA”) slightly angled laterally (towards the UOA) and posteriorly. Here the UOA is partially covered with a piece of Gelfoam. d Current Source Density analysis (CSD; Left) and MUA (Right) signals recorded through the depth of V1 in LEA-P2 in response to phasic UOA photostimulation (pulse parameters: 100 ms pulse duration, 5 Hz, 0.82 mW/mm 2 ; pulse periods denoted as blue bars above MUA plot). Here, all 100 needle-aligned µLED sites (“whole µLED array” condition) were activated simultaneously. CSD responses to each 100 ms pulse were zero-aligned ( n = 170 pulses), while MUA is shown for the full 5 Hz pulse train ( n = 34 trials). The dashed lines in the CSD panel demarcate the borders of layer 4 C (L4C); the gray shaded region in the MUA panel delimits the extent of L4C. e Same as in d , but following surface photostimulation of V1 via a laser-coupled optical fiber with pulse parameters of 10 ms, 5 Hz, 2.2 mW/mm 2 ( n = 160 pulses, 32 trials). f – i Top: relative cortical depth of each contact on LEA-P2 (black dot in the insets) is plotted versus the relative response (% firing rate increase over baseline) to UOA stimulation for different 450 nm µLED illumination patterns (top insets) ( n = 125–205 pulses per condition). Different colored traces are data for different photostimulation intensities (expressed as voltage or percent of max intensity used). Gray area: extent of L4C; dashed lines: approximate location of the L4A/4B (upper) and L5/L6 (lower) borders. In all panels, error bars represent standard error of the mean. Bottom: PSTHs with and without µLED activation are shown for the same contact on the LEA in L4C (marked by the black circle in the graphs above) across conditions. Dashed line in the PSTH: pulse periods. In all panels, error bars represent standard error of the mean.

    Article Snippet: For the CSD analysis shown in Fig. , current source density (CSD) was calculated from the band-pass filtered (1-100 Hz) and pulse-aligned and averaged LFP in response to the first pulse in a train (to avoid adaptation effects), using the kernel CSD toolbox (kCSD Matlab) .

    Techniques: In Vivo, Expressing, Activation Assay