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Fiji-macros

Miscellaneous of Fiji macros. To use save the relevant .ijm file locally and run it as a macro in Fiji.

Image saving

[czi_to_tiff.ijm] Batch process all files in a folder and save them by converting from .czi images (Bioformats) to .tiff format

[save_all_open.ijm] Save all open images in .tiff format in an output folder of choice

[save_separate_channels.ijm] Batch process all .tiff files in a folder and save 3 channels separately

Image pre-processing

[clahe_stack.ijm] Apply local contrast enhancement (CLAHE) to a Z-stack

[segment_nuclei_threshold.ijm] Batch process all files in a folder and segment blobs (nuclei) in .tiff single channel images by auto-thresholding. The input and output file name pattern can be defined by the user.

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