Sample data for "Live Cell Fluorescence Microscopy – An End-to-End Workflow for High-Throughput Image and Data Analysis"
Contributors
Researcher:
- 1. Department of Functional Organization of Biomembranes, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic.
Description
This repository contains:
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Sample data for the "Live Cell Fluorescence Microscopy – From Sample Preparation to Numbers and Plots" methodology paper by Zahumensky & Malinsky. The paper describes the preparation of live yeast cell samples for microscopy, the subsequent semi-automatic analysis of the microscopy images using our custom-written Fiji macros, and automatic processing of the output (Results table) from the image analys using custom-written R scripts. The data provided here are real experimental data from two publications of our group: Zahumensky et al., 2022 and Vesela et al., 2023
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"Results tables" from the Fiji based analysis
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Outputs of the processing of these Results tables using our R scripts, in the form of summary tables, graphs, and statistical analyses
Files
results_of_Fiji-based_analysis_of_sample_microscopy_data.zip
Additional details
Related works
- Describes
- Workflow: 10.17504/protocols.io.8epv5r23dg1b/v1 (DOI)
- Workflow: 10.1101/2024.03.28.587214 (DOI)
- Is published in
- Journal article: 10.1128/spectrum.01961-22 (DOI)
- Journal article: 10.1242/jcs.260554 (DOI)
Software
- Repository URL
- https://github.com/jakubzahumensky/microscopy_analysis
- Programming language
- ImageJ Macro, R
- Development Status
- Active
References
- Zahumenský, J., Mota Fernandes, C., Veselá, P., Del Poeta, M., Konopka, J. B. and Malínský, J. (2022). Microdomain Protein Nce102 Is a Local Sensor of Plasma Membrane Sphingolipid Balance. Microbiol. Spectr. 10, e0248922.
- Vesela, P., Zahumensky, J. and Malinsky, J. (2023). Lsp1 partially substitutes for Pil1 function in eisosome assembly under stress conditions. J. Cell Sci. 136, jcs260554.