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 (Stapel et al Documentation.pdf) contains details on:
- PathFinder Fiji plugin
- Cell annotation plugin in Fiji
- Transcript analysis plugin in Fiji
Additionally one can find detail on the KNIME workflow here