Data · dataset · 2019
Neurophotonics tutorial on making connectivity diagrams from Channelrhodopsin-2 stimulated data
Listed in Borealis and Agri-environmental Research Data Dataverse — shown once because both records carry DOI 10.5683/sp2/cchovv
This package of sample data and matlab codes will process, filter, and average raw voltage sensitive dye images, generate a comprehensive connectivity matrix and a network diagram (as seen in Lim et al., 2012, 2014).
Description
Requirements: Matlab (with Bioinformatics Toolbox and Brain Connectivity Toolbox) Inputs: sample data; Matlab functions; Mask.tif (as included in .zip file) Outputs: dF/F0(%) VSD connectivity matrix; Figure of network properties as a function of threshold levels; Network diagram To use this package: Unzip data files and ensure all Matlab functions are in the same directory as the NetworkAnalysis_VSD.m Open NetworkAnalysis_VSD.m with Matlab In NetworkAnalysis_VSD.m, enter the folder name where the data is stored (line 5) Execute code.
See corresponding articles: Lim et al.(2012). In vivo Large-Scale Cortical Mapping Using Channelrhodopsin-2 Stimulation in Transgenic Mice Reveals Asymmetric and Reciprocal Relationships between Cortical Areas. Front Neural Circuits 6:11.
Read the rest (3 more)
Lim et al.(2014). Optogenetic mapping after stroke reveals network-wide scaling of functional connections and heterogeneous recovery of the peri-infarct. J Neurosci 34:16455-16466.
See also: Brain connectivity toolbox: sites.google.com/site/bctnet/ Rubinov and Sporns (2010). Complex network measures of brain connectivity: uses and interpretations. Neuroimage 52:1059-1069.
Diana Lim and Jeffrey LeDue, University of British Columbia, 2015.
Links
Where it is published
- Dataverse dataset page borealisdata.ca/dataset.xhtml?persistentId=doi%3A10.5683%2FSP2%2FCCHOVV ↗
landing page · from borealisdata ca
- DOI doi.org/10.5683/sp2/cchovv ↗
DOI / persistent id · from borealisdata ca
Catalogue records · 1
- Dataverse API borealisdata.ca/api/datasets/:persistentId/?persistentId=doi%3A10.5683%2FSP2%2… ↗
metadata API · from borealisdata ca
Topics
- Stated by source
- Medicine, Health and Life Sciences · Medicine, Health and Life Sciences
- From keywords
- Chemistry · Computer Science & AI · Earth & Environmental Science · Economics & Finance · Engineering · Humanities · Life Sciences · Life Sciences · Mathematics & Statistics · Medicine & Health · Medicine & Health · Ocean & Atmospheric Science · Social Science
- Inferred from text
- Biochemistry and cell biology 71% · Image 65%
Provenance · 2 source records, 23 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Borealis | doi:10.5683/SP2/CCHOVV | 12 d ago | JSON v1 |
| Agri-environmental Research Data Dataverse | doi:10.5683/SP2/CCHOVV | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:group:3101 | enrichment · borealisdata ca | taxonomy-embedding@1.0.0 | title+keywords+description (71%) |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /subjects |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:chemistry | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:computer-science-ai | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:earth-environmental | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:economics-finance | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:humanities | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · borealisdata ca | connector:borealisdata_ca@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:mathematics-statistics | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · borealisdata ca | connector:borealisdata_ca@1.0.0 | /subjects |
| concepts[field].local:field:ocean-atmospheric | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:social-science | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[modality].local:modality:image | enrichment · borealisdata ca | keyword-concept-rules@1.0.0 | title+description (65%) |
| created_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| description | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /description |
| publication_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| title | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /name |
| updated_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| version_label | source · borealisdata ca | connector:borealisdata_ca@1.0.0 |