Welcome to the PEG10 Image Analysis project!

This code is for the eLife article "UBQLN2 restrains the domesticated retrotransposon PEG10 to maintain neuronal health in ALS" by the Alex Whiteley lab.

Usage

1. First clone the Git repository to a location on your computer

   git clone https://github.com/jwtay1/PEG10-image-analysis.git

2. In MATLAB, add the new folder to the path (e.g., by right clicking in the Current Folder panel and selecting Add to Path > Current Folder)

3. Edit the script exportND2asTIFs.m to change the paths for the input and output folders. The input folder should point to the folder where the ND2 files are (the ND2s can be in subfolders under this).

4. Run the script. This should generate a series of TIF files which are reduced in size (by calculating the mean in 2x2 blocks).

5. Edit the script exportMask.m and change the dataDir and outputBaseDir paths. The dataDir variable should point to the output path of the exportND2asTIFs script.

6. Run the script. This should generate a series of TIFs containing masks which label each pixel in the image as being part of the region of interest (true) or background (false).

7. Edit the masks if necessary, e.g. using Fiji/ImageJ. If using ImageJ, you will need to invert the LUT and then invert the image to get the final mask.

8. Edit the script processFilesWithMask.m and change the dataDir, maskDir, and outputDir as appropriate.

9. Run the script. The code should output a series of PNG images showing the outline of the regions of interest in green. A MAT-file will be produced containing intensity of the PEG10 and Map2 channels.

10. Finally, edit the script export2csv.m to modify the dataDir. This should point to the locatin of the MAT-files.

11. Run the script to obtain a CSV file with a summary of all the measured intensities. Note that in the CSV file, Texas Red is the PEG10 and Cy5 is the Map2 channel.

Acknowledgements

If you use this code in a publication, please cite our paper:

Black et al. "UBQLN2 restrains the domesticated retrotransposon PEG10 to maintain neuronal health in ALS." eLife 79452 (2023). doi: https://doi.org/10.7554/eLife.79452.