Advice for use: These microscopy experiments are designed analyzed by the csat_calcs module which is under heavy construction. The checklist below outlines the steps to initiate an experiment repository in a tidy manner and add the analysis submodule. Any changes to the analysis module should be committed in a non-breaking manner, as they link to the main branch. Where experiment specific changes are required, consider creating a new csat_calcs branch. Please check off the tick boxes as you go.
- uncomment raw_data folders in gitignore
- delete placeholder files in image and raw_data folders
- upload raw data
- activate csatCalculations (conda) environment and import editable analysis submodule in vscode terminal:
git submodule add https://github.com/ocarmo/210805_csat-calculations.git csat_calcs
- update header and fields below
Purpose: Collecting before/after intensity data for constructs specified in the repository
Cell Type: Neuro2a cells
Instrument/techniques: LSM900, experiment block set up, 10% excitation for 40.51 sec, acquisitions at mCh 0.6% 600V.
Data produced: See python results folder
Analysis:
- scrape important details of metadata
- cell identification and maping cells from before to after image
- pixel information collection
- data fitting
- determine csat
- plot csat and tile images to plot before and after mCh in grayscale
References/Resources: Shin et al. 2017, http://dx.doi.org/10.1016/j.cell.2016.11.054