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Batch-processing-toolkit

This repository includes hands-on FIJI macros mainly for image batch processing.

Table of contents:

  1. Downsampling and upsampling
  2. Split RGB channels

1. Downsampling and upsampling

ImageJ/FIJI Macro - This script is used for batch downsampling and upsampling.

Specification:

Input - 2D .tif or .tiff 8-bit raw hr images saved in one folder.
Output - Five folders:

  • Folder 1 - hr: your input 8-bit images
  • Folder 2 - hr_RGB: result of converting input 8-bit images into RGB format
  • Folder 3 - lr: Downsampled RGB images (Downsampling method: None; Scale: 4X)
  • Folder 4 - bicubic_upsampling: upsampled RGB images (Upsampling method: bicubic; Scale: 4X)
  • Folder 5 - bilinear_upsampling: upsampled RGB images (Upsampling method: bilinear; Scale: 4X)

Note: All the upsampled images use None downsampled images (i.e. images in Folder 3) as input.

2. Split RGB channels

ImageJ/FIJI Macro - Batch splitting 2D RGB .tif/.tiff images into single channels and save them in 3 different folders

Specification:

Input - 2D RGB .tif or .tiff images saved in one folder.
Output - Splitted single channel images saved in three folders, each of which contains images of one single channel.

How to use:

  • Put all your images in one folder.
  • Simply drag and drop the .ijm file into ImageJ/FIJI.
  • Click "Run".
  • When the dilog window pops up, select the folder where you put all your images as the target directory.
  • Then you are done! Check the spliited single channel images in different folders that are just automatically created!