š§µ New protocol out in @cp-starprotocols.bsky.social! Step-by-step guide to infer forces in tissues using ForSys, by @borgesaugust.bsky.social, Jeronimo Miranda, Alberto Ceccarelli, Guilherme Ventura,
@kuba-sedzinski.bsky.social, @hernanlopez-schier.bsky.social and I,
www.cell.com/star-protoco...
Check out this amazing conference of Mathematical Biology! Great speakers, venue and city!!
Osvaldo Chara
Osvaldo Chara
Scripting is also easy! Load your images into Frame objects, then pass them to ForSys: import forsys as fs ā build frames{} per timepoint ā forsys = fs.ForSys(frames) and then infer. Works for both experimental š¬ and in silico š» data!
Would you like to run our Cellular Potts Model (#CPM) of neuromast regeneration in #zebrafish? It is now available in the amazing @morpheus-lab.bsky.social repository:
morpheus.gitlab.io/model/m4377/
Curious about the Science? Check our paper: doi.org/10.1016/j.jt...
ForSys is an open-source Python tool for non-invasive stress inference from microscopy images. It comes with 3 usage options: a Fiji GUI š„ļø, a Command Line Interface āØļø, and full Python scripting š. Use what you need!
GUI users: install the ForSys plugin in Fiji via HelpāUpdateāManage Update Sites. Add sites.imagej.net/ForSys, restart, then open PluginsāForSys. Point it to your image folder, set your conda environment, and hit Run! No coding needed.
Thanks to all co-authors, labs, and collaborators! ForSys is free & open source. Find the detailed usage description in the Protocol (www.cell.com/star-protoco... and the code, example notebooks & full docs here: github.com/borgesaugusto/forsys Happy inferring! š«§š¬
CLI users: activate your forsys environment, then run one command! Static: python -m forsys -f /data -m nnls -sf /resultsv or for Dynamic inference: add ādynamic. Full flag list via -h or in the docs at forsys.readthedocs.io.
Check all details behind ForSys and its validation in our bsky.app/profile/cp-i... publication: www.cell.com/iscience/ful.... This protocol focuses on how to actually run it, step by step
Amazing paper in @pnas.org of @yanlanmao.bsky.social lab featuring @giuliapaci.bsky.social and colleagues!!
