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Original MediaWiki page

MS-ECS-2D update site

The content of this page has not been vetted since shifting away from MediaWiki. If you’d like to help, check out the how to help guide!

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