KymoAnalyzer Software for the Analysis of Intracellular Transport

KymoAnalyzer is a semi-automated ImageJ software package of macros designed to quantify parameters that describe the intracellular transport of fluorescent cargoes and/or molecular motors from time-lapse live-imaging sequences in neuronal projections, or from in vitro motility assays.

KymoAnalyzer generates kymographs from time-lapse movies, guides the user in the manual assignment of particle trajectories from kymograph images, and automatically calculates multiple transport parameters. It can process large movie datasets and provides user-friendly data output stored in text files that can be imported into common spreadsheets or statistical software.

 

KymoAnalyzer is an open-source macro that is 

freely available and can be modified to adapt to other users’ requirements. We also provide a detailed operation manual describing the step-by-step procedure for using the KymoAnalyzer package.

Click here to download KymoAnalyzer v1.01

Click here to download the user manual

If you use KymoAnalyzer in a publication, please cite the article in which the software was described:

 

Neumann S, Chassefeyre R, Campbell GE, Encalada SE. KymoAnalyzer: a software tool for the quantitative analysis of intracellular transport in neurons. Traffic, 2017 Jan;18(1):71-88. doi: 10.1111/tra.12456. Epub 2016 Dec 11.

 

We encourage users to modify the open source code and/or develop plugins/macros to extend the applicability of KymoAnalyzer to the analysis of various datasets, including combining this with particle detection/tracking algorithms. If you modify the KymoAnalyzer, please contact us (encalada@scripps.edu) so that we may add new plugins/macros to our website link along with your documentation.

Version History:

v. 1.00 - Release

v. 1.01 – Bug fixes

Change-log

Adjust sorting parameters in 6_poolData.ijm to allow for analysis of very slow cargos (those between 0 and 0.1 µm/sec)

 

6_poolData.ijm

4a Pooled Segmental Velocities

-Changed Ant. and Ret. thresholds for sorting from |0.1| to |0|

4b Pooled Combined Segmental Velocities

-Changed Ant. and Ret. thresholds for sorting from |0.1|to |0|