KymographBuilder : Yet Another Kymograph Fiji plugin
|Development status||v1.2.2, stable|
KymographBuilder is Yet Another Kymograph Fiji plugin.
Features are :
- Build kymograph from a straight or segmented line (a polyline).
- Build kymograph for images with multiple channels.
- Take into account the width of the line using maximum projection along its thickness.
- Built from scratch and use the ImageJ2 Ecosystem.
- Fast and easy to use.
How to use :
- Draw a line: it can be a polyline and you can also set the thickness that will be taken into account by the plugin.
- Launch KymographBuilder : ▶ ▶
- You're done.
You can script the plugin. Here is an example :
# @Context context # @Dataset dataset # @ImageJ ij # @LogService log # This script exemplifies how to instruct KymographBuilder to # process all the line ROIs present in the ROI Manager. For more # details see http://imagej.net/KymographBuilder import ij.plugin.frame.RoiManager as RM import sc.fiji.kymographBuilder.KymographFactory as KFactory def validDataset(dataset): """Assess if dataset has suitable dimensions""" from net.imagej.axis import Axes z = dataset.dimension(dataset.dimensionIndex(Axes.Z)) t = dataset.dimension(dataset.dimensionIndex(Axes.TIME)) return z * t > 1 rm = RM.getInstance() counter = 0 if validDataset(dataset) and rm and rm.getCount(): for roi in rm.getRoisAsArray(): if roi.isLine(): kfactory = KFactory(context, dataset, roi) kfactory.build() counter += 1 title = "Kymograph" + str(counter).zfill(3) + "_" + roi.getName() ij.ui().show(title, kfactory.getKymograph()) log.info("MultiKymographBuilder Finished. " + str(counter) + " ROIs processed") else: log.error("Either the ROI Manager is empty or " + dataset.getName() +" has invalid dimensions")
- Multi_Kymograph : The first kymograph bundled with Fiji, with support for multiple Line ROIs
- Source code on GitHub : https://github.com/fiji/KymographBuilder
- Maven : https://maven.scijava.org/#nexus-search;quick~kymographbuilder
- Travis CI : https://travis-ci.org/fiji/KymographBuilder
KymographBuilder has been created by Hadrien Mary.
This work started in 2016 at the Gary Brouhard laboratory (http://brouhardlab.mcgill.ca) at McGill University.