fiji-convert-bin-project

For questions please contact: tischitischer@gmail.com

This repository conatins a Fiji script to process a folder of image stacks and save them in a different file format, binned, different bit-depth and x,y,z projections.

credits

The code for x,z,y projection is taken from here: http://www.masny.dk/imagej/max_xyz_project/index.php

installation

• install fiji: https://fiji.sc/
• download and extract this repository: https://github.com/tischi/fiji-convert-bin-project/archive/master.zip
• move the .jar files to Fiji's plugin folder
• You need the HDF5 plugin
  • [Fiji > Update > Manage Update Sites] [X] HFD5

run it

• drag the fiji-convert-bin-project.py script onto Fiji and [Run]
• it first asks for a parameter file, which you got from previous runs; initially you will not have one, so you click Cancel

parameters

• ...
• binning_x, binning_y, binning_z

usage notes and tips

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