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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