FIM Imaging & FIMTrack

FIM imaging can be used in a wide range of applications (e.g. tracking animals, measuring the growth of roots, etc.). The below linked web site shall help other groups to construct, buy or use such a setup. Our research focus is the motion analysis of crawling Drosophila larvae. Thus we will introduce FIM and FIM-related software for tasks dealing with larval tracking. We've developed FIMTrack for high-throughput Drosophila larvae tracking for example. However the FIM setup can also be used other purposes.

For more information please visit the FIM website.

 Hardware: FTIR-Based Imaging Method

© CVMLS

 We utilise frustrated total internal reflection (FTIR) to image the contact surface of the target and the surface medium, therefore this technique is called FTIR-based Imaging Method (FIM). For this purpose, infrared (IR) LEDs are placed around an acrylic glass plate. Because of different optical densities of air and acrylic glass, the light enters the glass and is completely reflected at the glass/air boundary (total internal reflection; TIR). For larval locomotion experiments a moist surface (e.g. agar) is placed on the glass. Again, the light enters the agar and is completely reflected at the agar/air and agar/glass boundary. The reflection angles change according to the refractive indices of the media. Given animals touching the agar, refracted light is now below the so-called critical angle: It is no longer totally reflected and can be captured by a camera from underneath.

Software: FIMTrack

© CVMLS

 To facilitate 2D locomotion quantification (i.e. tracking) we developed FIMTrack. FIMTrack processes images recorded using a FIM setup to calculate posture and motion related parameters. Although this tracking program is designed for Drosophila larvae, it is also tested for C. elegans worms and planaria.

FIMTrack is available for all operating systems (MS Windows, Mac OS and Linux). A user- friendly graphical interface allows easy interaction with the program. Beside the calculation of the trajectories, there is another module to get detailed informations about the results (called Results Viewer). This module includes the table with all calculated features, images with highlighted posture and motion related features and a plotting functionality. Furthermore, advanced manual tracking can be done easily. 

Available Movement Features

Features calculated by FIMTrack can be divided into primary features (based on the contour), secondary features (based on the primary features) and tertiary features (based on primary features and time). In addition, several stimulus related points, lines and regions can be set via drag and drop which are used to calculate stimulus-related features such as distance to stimulus etc.

Primary Features:

  • Momentum
  • Heat and tail points
  • Several spine points
  • Spine point radii
  • Area
  • Perimeter

Secondary Features:

  • Body bending angle
  • Spine length
  • Is left/right bended indicator
  • Is coiled indicator
  • Distance to stimulus
  • Is in stimulus region indicator

Tertiary Features:

  • Movement direction Velocity
  • Acceleration
  • Accumulated distance
  • Distance to origin
  • Bearing direction
  • Stop/go phase indicator

Additional Information

Since FIM imaging can be used in a wide range of applications (e.g. tracking animals, measuring the growth of roots, etc.), this web site shall help other groups to construct, buy or use such a setup. Our research focus is the motion analysis of crawling Drosophila larvae. Thus we will introduce FIM and FIM-related software for tasks dealing with larval tracking. We've developed FIMTrack for high-throughput Drosophila larvae tracking for example. However the FIM setup can also be used other purposes.

Photos

FIM image gallery
© CVMLS
  • FIM image gallery
    © CVMLS
  • FIM image gallery
    © CVMLS
  • FIM image gallery
    © CVMLS
  • FIM image gallery
    © CVMLS
  • FIM image gallery
    © CVMLS
  • FIM image gallery
    © CVMLS
  • FIM image gallery
    © CVMLS

Downloads

Here you can find the download links for FIMTrack v1 and v2 as binary packages, as well as some supplementary material.

Changelog

  • (31.01.2018) Several datasets are now available. Feel free to use this data for evaluation purposes in your scientific work. If you use our data, please be sure to cite the associated publication.
  • (28.11.2016) An updated version of the standalone FIMTrack program for Mac OS X (X64; i5/i7) is now available.
  • (19.08.2016) There may be are some problems regarding the standalone version of FIMTrack and Mac OS X 10.10 and 10.11. However, you could try to build FIMTrack from source by following the instructions provided at Github or you could try the Windows version.
  • (04.02.2016) Second update of the recommended Mac OS and Windows versions. Several Bugs are removed. OpenCV is updated to version 2.4.11 and the UI uses now Qt 5.5.1.
  • (24.09.2014) Recommended Mac OS and Windows version are updated. Several Bugs are removed and new features are added.
  • (06.06.2014) Mac OS versions are precompiled for Mac OS 10.9 (Mavericks) only because of an incompatibility of Qt (v.4) and C++11 in older Mac OS systems.
  • (06.06.2014) New Larva tap added to the results viewer for basic plotting. Larva tab is integrated into Windows and Mac OS 10.9 i5/i7 version. Plots in the larva tab uses QCustomPlot The manual will be updated soon.

FIMTrack v2

(Recommended)

Version Link
Windows (x86) Fimtrack V2 Windows (x86)
MacOS (x64 i5/i7) Fimtrack V2 MacOS (x64)
MacOS (x64 Dual-Core) Fimtrack V2 MacOS (x64 Dual-Core)
Manual Fimtrack V2 Manual
Sources

The source code of FIMTrack is available at Github. FIMTrack has been build and tested successfully on recent Linux Mint systems, Mac OS X Mavericks as well as Windows 7.

FIMTrack v1

(Archived)

Version Link
Windows (x86) Fimtrack V1 Windows (x86)
MacOS (x64) Fimtrack V1 MacOS (x64)
Manual Fimtrack V1 Manual

Supplementary

File Link
FIM Test Imags Test Img

Datasets

We provide additional datasets that can be used in combination with FIMTrack for testing or evaluation purposes. For our other datasets, see Datasets

Tracking Validation Dataset

The following dataset was used for validation in the publication: Risse B, Berh D, Otto N, Klämbt C, Jiang X (2017) FIMTrack: An open source tracking and locomotion analysis software for small animals. PLOS Computational Biology 13(5): e1005530.

Fimtrack Validation Data + MATLAB Scripts