What is this repository for?

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. Details can be found in

• B. Risse, S. Thomas, N. Otto, T. Löpmeier, D. Valkov, X. Jiang, and C. Klämbt, "FIM, a Novel FTIR-Based Imaging Method for High Throughput Locomotion Analysis," PLoS ONE, vol. 8, no. 1, p. e53963, Jan. 2013.

• Risse, B., Jiang, X., & Klämbt, C. (2013). FIM: Frustrated Total Internal Reflection Based Imaging for Biomedical Applications. ERCIM News, 95(Image Understanding), 11-12.

• B. Risse, N. Otto, D. Berh, X. Jiang, and C. Klämbt, "FIM Imaging and FIMTrack: Two New Tools Allowing High-throughput and Cost Effective Locomotion Analysis," Journal of Visualized Experiments: JoVE, no. 94, p. e52207, 2014.

• B. Risse, D. Berh, N. Otto, X. Jiang, and C. Klämbt, "Quantifying subtle locomotion phenotypes of Drosophila larvae using internal structures based on FIM images," Computers in Biology and Medicine, vol. 63, pp. 269-276, 2015.

For more informations contact fim[AT]uni-muenster[DOT]de

This FIMTrack fork extends the original version with some additional functionality like automatic adjusting of thresholds for each frame based on assisted data (e.g., [DeepLabCut](https://github.com/DeepLabCut/DeepLabCut tacking), visual tracing and debugging of the thresholds inference, import of video in addition to image loading, output results extension.
By Artem Lutov <[email protected]>
Affiliation: UNIFR, Lutov Analytics

Known Forks

• An extension of the latest original FIMTrack aimed for fish tracking: https://github.com/wildner/FIMTrack_extension
• A refined version of an outdated FIMTrack: https://github.com/kostasl/FIMTrack

Building FIMTrack

To clone this repository with submodules use:

$ git clone --recursive <repo_url>

It fetches QCustomPlot (ver. 1.3.2) submodule. To fetch submodules after the non-recursive clone, execute:

$ git submodule update --init --recursive

Linux

These are instructions for Ubuntu/Debian systems, the packages should be similar on other distributions.

Dependencies

$ sudo apt-get install git libopencv-dev libhdf5-dev qt5-default g++

Build

Execute from the repository directory:

qmake
make -j 4

To build debug version: make debug -j 4

To execute the built app:

$ build/release/bin/FIMTrack

To execute debug version: build/debug/bin/FIMTrack

Mac OS X

Either use the same workflow as Linux Build or perform the build with Xcode and Homebrew.

Dependencies

• Git
  • sudo brew install git
• OpenCV
  • sudo brew tap homebrew/science
  • sudo brew install opencv --c++11
• Qt
  • sudo brew tap homebrew/versions
  • sudo brew install qt5
  • sudo brew link --force qt5

Ensure that OpenCV v4 is installed and its headers are located in /usr/local/include/opencv4:

$ sudo ln -s `find /usr/local -name "opencv4" -type d | grep "/include/"` /usr/local/include/opencv4