thorimage-sync_2p-analysis
Notebook to analyze ThorImage + ThorSync 2-photon data with light stimulation.
Science Score: 54.0%
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Low similarity (4.9%) to scientific vocabulary
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Repository
Notebook to analyze ThorImage + ThorSync 2-photon data with light stimulation.
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Metadata Files
README.md
ThorImage/ThorSync_2P-analysis
Notebook to synchronize and analyze ThorImage + ThorSync 2-photon calcium imaging data with light stimulation.
The notebook requires the user to draw ROIs as described here. The ROIs are drawn on an automatically computed sum projection. The stimulation information is automatically obtained from the ThorSync file.
Output returned by notebook:
1. Dataframe containing information per frame in the format:
Channel + Sample | Filename | Frame |Mean pixel value in ROI | Mean pixel value in bkg area | NormmeanpixelvalueinROI | Time passed (s) | dF/F0 | LED (ON/OFF)| -------------------|------------------|-------|------------------------|------------------------------|------------------------------|------------------|-------|-------------| ChanA (001001001)| ChanA001001001| 1.0 |542.6812468577175 | 541.7430997876858 |0.9381470700317323. | 0.0 | 0.95 | 0 | . . . | . . . | . . . |. . . | . . . |. . . | . . . | . . . | . . . |
2. Pickled dictionary containing raw and analyzed data, including ROI coordinates
3. dF/F0 over time showing stimulation:
The notebook also returns raw mean and background normalized mean traces.
4. dF/F0 heatmap (sum over all frames):
5. dF/F0 heatmap movie over time showing stimulation:
https://user-images.githubusercontent.com/56094636/156097148-af4bfca4-12b5-4a44-889d-0c9e73c04b46.mp4
6. ROIs drawn for area of interest and background:
Owner
- Name: Laura Luebbert
- Login: lauraluebbert
- Kind: user
- Company: @pachterlab
- Website: www.lauraluebbert.com
- Twitter: NeuroLuebbert
- Repositories: 18
- Profile: https://github.com/lauraluebbert
Ph.D. candidate in the @pachterlab at Caltech · Author of gget
Citation (CITATION.cff)
authors:
- family-names: Luebbert
given-names: Laura
orcid: "https://orcid.org/0000-0003-1379-2927"
cff-version: 1.2.0
date-released: "2022-02-28"
identifiers:
- description: "DOI"
type: doi
value: 10.5281/zenodo.6317384
license: MIT
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/lauraluebbert/ThorImage-Sync_2P-analysis"
title: "ThorImage-Sync_2P-analysis"
version: 0.0.1
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