This is an archive of the old MediaWiki-based ImageJ wiki. The current website can be found at

MS-ECS-2D update site

This page provides a detailed explanation and pointers towards the use of the MS-ECS-2D update site. It is made available in conjunction with the publication of the paper:

Stapel, L. C., Lombardot, B., Broaddus, C., Kainmueller, D., Jug, F., Myers, E. W., & Vastenhouw, N. L. (2015). Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos. Development, dev-128918.

The documentation (File:Stapel et al Documentation.pdf) contains details on:

  • PathFinder Fiji plugin
  • Cell annotation plugin in Fiji
  • Transcript analysis plugin in Fiji

Additonnally one can find detail on the KNIME workflow here