README.md

faim-ij1-io

A simple ImageJ2/SciJava wrapper for reading and writing TIFF (and similar) files through IJ1

This repository is a minimal wrapper around the ImageJ1 TIFF IO functions (namely IJ.openImage and FileSaver#saveAsTiff) to make them available as headless-compatible SciJava commands.

This component mainly exists because of two long-standing issues:

• Poor handling of Metamorph nd/stk datasets by bio-formats
  • ome/bioformats#3032
  • ome/bioformats#3578
  • ome/bioformats#3586
• Poor TIFF reading/writing performance of SCIFIO
  • scifio/scifio#7
  • scifio/scifio#310

So in order to make KNIME workflows using one or both of the above have an (at least) acceptable performance 😢, we need to fall back to ImageJ1 IO.