ENCALADA LAB
Endolysosomal Membrane Trafficking and Neurodegeneration
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.
Download KymoAnalyzer:
You can dowload KymoAnalyzer from this link, where you will also find the KymoAnalyzer Manual, and also a MATLAB file that you can use to process your data:
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|
Troubleshooting KymoAnalyzer
When running the Segments macro, if you encounter the following error:
It is likely you drew horizontal trajectories in the kymograph, which KymoAnalyzer cannot analyze. Re-draw trajectories in your kymographs and re-run the Segments macro.