Need help or advice ? Come to the Icy club ! - Every Wenesday morning from 9h30 to 12h30 - Francois Jacob Building - Main hall - Pasteur
Register

User reviews

This plugin is not rated yet


Please log-in to post a review

CapillaryTrack

by Frederic Marion-Poll

Build kymographs to monitor the evolution of the level of a liquid in capillary tubes (Java 8)

Publication Id
ICY-V5N6C4
See technical details
View complete changelog

Documentation

Warning: to install and run this plugin, you need Java 8, java 1.8 SDK. Update your Java environment to the latest version (this message was written on March 7, 2017)

Capillarytrack is meant to analyze images where 20 capillaries filled with a liquid can be consumed by flies. A webcam placed over this box takes 1 image per min. We want to follow the liquid level across time. The idea is to place ROI line over each capillary and to follow the profile of the pixels over time using kymographs. The plugin allows to:

- read a stack of jpg files or an AVI in "virtual" mode (images read are "buffered" in a separates thread)

- place an array of line ROIs over the image

- generate an array of kymographs corresponding to the profile of each line across time

- filter the kymographs

- detect a path from each kymograph (using an adjustable threshold) over the raw data or the filtered data and export the results to Excel.