Version 1.1.1 — 15/03/202-

  • Major Update
  • Previously the tracing algorithm called the decision module only when 2 or more possible future tracks were found. We changed the algorithm so that it would also call the module when no future path is available. This has the effect that small gaps in the kymographs are closed more efficiently than before, increasing performance of KymoButler by about 3%.
  • A new network was trained on a larger dataset of kymographs to boost performance
  • An ImageJ plugin was developed by Fabrice Cordelieres from the University of Bordeaux. Try it here: https://github.com/fabricecordelieres/IJ-Plugin_KymoButler_for_ImageJ
  • Please have a look and give us feedback!

Version 1.0.2 — 21/08/2019

  • Due to increasing demand we had to decrease the maximum allowed number of pixels to 150,000
  • We also added a timeout counter for exceedingly long computations (larger than 30 sec)
  • Added a extra column in the summary.csv file that gives the chosen threshold
  • optimised the code to be faster

Version 1.0.1 — 19/08/2019

Added new column to the summary.csv file that contains the start to end velocity additionally to the already shown average frame to frame velocity.

Version 1.0 — 15/07/2019

KymoButler is finally out of beta! Version 1.0 is described in our paper: https://www.biorxiv.org/content/10.1101/405183v3. Please drop us an email if you need access to older versions. Have fun!

Minor changes during the revision process were the following:

  • The webform now allows for quick parameter changes on one page. For example, if no tracks are found one can just adjust the threshold and try again without re-uploading the kymograph
  • We added a new output file that quantifies particle velocities, particle track duration, total track displacement, pausing time, and number of reversals. In order to get biologically meaningful quantities you have to provide the pixel size along the y-axis (time) and the x-axis (space).
  • KymoButler now assigns track overlaps to the track that has the highest probability to be found in the overlap region.
  • You can now discard tracks that below a certain size and/or visible for less than a certain frame number.