This repository contains scripts to the manuscript titled ‘Generation of 3D human foetal testis reconstitutions for in vitro culture.’
The repository contains scripts in Python, in R and one for Adobe Photoshop.
The Python scripts were used to pipeline microscope image files (.ims or .tif). Inside each script are detailed instructions for use.
- These scripts were written by J. van der Ster.
- The ‘Gray_normTIFF’ script normalizes the signal and grayscales all .tif files from in your specified folder. This is useful for 2D .tif images generated by FIJI.
- The ‘Gray_norm_mip_scalebarTIF’ script processes .ims files by separating the channels into 4 .tif files, performs maximum intensity projection (MIP), normalizes the signal and generates a scalebar .tif file from the metadata inside the .ims file. This is useful for (small) 3D .ims images to quickly obtain .tif files and the scalebar for Photoshop.
The R scripts were used to generate plots from Excel files containing quantification data collected through Imaris.
- Each subfolder indicates the Figure in the manuscript for which the script was used.
- ‘Fig2B’ contains the R file alongside 4 .xls files generated by Imaris (and deleting the first row). The R file plots the data into a violin plot.
- ‘Fig2CEG’ contains the R file alongside a results data .xls file. The R file plots the absolute DDX4 count, log-normalized DDX4 count and the volumes of reconstitutions with color codes for different parameters inside the .xls file.
- ‘Fig3H’ contains the R file alongside 4 .xls files with results data. The R file plots log-normalized germ cell count per donor into one dot plot, with color codes and shapes for the different parameters in the .xls files.
Finally, the 'TIFF_to_Photoshop' folder contains a script to run in Adobe Photoshop. This script automatically takes the .tiff files in the input folder and combines them in a template file (also provided) in an output folder. The .psd files can then be used for brightness/contrast adjustments.
- This script and attachments were written by A.W. Overeem.
- The folder contains its own instructions in the Readme file.
- The folder also contains example .tiff files from the manuscript to test out the script on your PC.