Semi-automated image analysis tool for fluorescence microscopy data from 12-well plates.
Most significant parts:
*5:15 - User interface in Fiji. Name your markers. Set your processing/analysis options.
*16:30 - First user interface in Matlab. Define your experimental groups.
*21:25 - Second user interface in Matlab. Check your results. Perform your statistics.
Full timeline:
3:45 - Start Fiji part. Select file to extract data from.
5:15 - User interface in Fiji. Name your markers. Set your processing/analysis options.*
8:50 - Text data produced by Fiji.
10:25 - Inspection of .czi raw data.
12:40 - Image data produced by Fiji.
14:30 - Start Matlab part. Select folder with data produced by Fiji.
16:30 - First user interface in Matlab. Define your experimental groups.*
21:25 - Second user interface in Matlab. Check your results. Perform your statistics.*
25:05 - Know your data. Understand artifacts and outliers.
28:35 - Example of t-test use.
30:00 - Nuclei number versus Myotubes number.
31:10 - Example of ANOVA use.
This tool is written to run in ImageJ/Fiji and Matlab. As an input, It uses scanned .czi files (with tiles, positions etc).
Data from signal intensity, thresholded objects and colocalization (ICA) analysis can be statistically analyzed and visualized.