pyFIM

Release:0.2
Date:Apr 25, 2018

pyFIM is a Python 3 package for analysis of FIMTrack data. It extracts parameters from .csv files produced by FIMTrack, performs additional analyses and facilitates comparison of experiments.

FIMTrack is an object tracker developed by Risse et al. (University of Muenster, Germany). From their Github repository:

“FIMTrack is a larval tracking program to acquire locomotion trajectories and conformation information of Drosophila melanogaster larvae. It is optimized for FIM images. FIM is an acronym for FTIR-based Imaging Method, whereby FTIR is the short form for Frustrated Total Internal Reflection.”

Core Features

  • import of .csv files
  • extraction of FIMTrack parameters
  • built-in additional high-level analyses
  • easy handling and comparison of experiments

Support

If you are having issues, drop me a message: pms70[AT]cam[DOT]ac[DOT]uk

License

pyFIM is licensed under the GNU GPL v3+ license

Acknowledgments

Big thanks to Dimitri Berh, Benjamin Risse, Nils Otto and Christian Klämbt for sharing their MatLab code.

FIMTrack References

Risse B, Berh D, Otto N, Klämbt C, Jiang X. FIMTrack: An open source tracking and locomotion analysis software for small animals. PLoS Computational Biology. 2017;13(5):e1005530. doi:10.1371/journal.pcbi.1005530.

Risse B, Otto N, Berh D, Jiang X, Klämbt C. FIM Imaging and FIMtrack: Two New Tools Allowing High-throughput and Cost Effective Locomotion Analysis. Journal of Visualized Experiments : JoVE. 2014;(94):52207. doi:10.3791/52207.

Risse B, Thomas S, Otto N, et al. FIM, a Novel FTIR-Based Imaging Method for High Throughput Locomotion Analysis. PLoS ONE. 2013;8(1):e53963. doi:10.1371/journal.pone.0053963.

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