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Pymagor aims to automate many of labor intensive steps of calcium imaging data analysis and provide a user friendly environment for manual ROI drawing. Pymagor can open any multi-page TIFF files (and other supported files, see below) and you can quickly check dF/F image (either as frame average or movie) and the basal fluorescence image for morphology (raw frame or frame average).
Pymagor can be used to open individual image files to quickly check the response etc. For this, you don't need to provide meta data (stimulus, field-of-view). You can set the frame ranges for F and stimulus periods in Parameter pane.
For more detailed analysis involving multiple files, organize your data in a simple spreadsheet (xls or csv) to provide meta data (stimulus condition, field-of-view, etc) to Pymagor. You can generate a template xls/csv file for your data folder from Pymagor (File menu) and fill in a few meta data manually. Alternatively, you can use online analysis sheet for registering meta data.
Opening a spreadsheet in Pymagor will launch Batch Launcher. Here you will choose files you want to analyze. Pymagor will align across trials (correcting slow tissue drift) and pack them into one image window where you can draw ROIs manually, get dF/F traces, and produce a multi page PDF summary report and also export these data to MATLAB as mat file for further analysis.
- Supported image file formats
- ScanImage 3.6 and 3.8 (Iori)
- Matlab exported tif (Iori)
- Micro-Manager tiff file (Otto)
- tif saved in ImageJ tiff file (Otto)
[Trial-Viewer] (https://github.com/i-namekawa/Pymagor/wiki/Trial-Viewer) screenshot
QuickPlot screenshot
