Zebrafish Image Processing Files

This software is supplementary material to a submitted paper

Christian Pylatiuk, Daniela Sanchez, Ralf Mikut, Rüdiger Alshut, Markus Reischl, Sofia Hirth, Steffen Just, Wolfgang Rottbauer: 
Automatic Zebrafish Heartbeat Detection and Analysis. 2014

It contains the following files: 

heartbeat.exe     - Program file for heartbeat analysis
vid2tif.m         - Program file for extraction of single frames from videos as tif files 
C-1.wmv           - Sample video
C-2.wmv           - Sample video
C-3.wmv           - Sample video
C-4.wmv           - Sample video

This software implements an in-vivo method for fully automatic detection and analysis of heartbeats in videos of non-fixed and non-anaesthetized zebrafish embryos. heartbeat.exe is free software. It is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of 
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 

This version requires an installed runtime version of the Matlab Compiler, version 8.1. (R2013a). This version is available free of charge for various systems (Windows 32/64 Bit, Linux, MAX). It can be downloaded from

http://www.mathworks.de/products/compiler/mcr/


Steps: 
1. Extract tif images from a video, 
   vid2tif.exe <Extension for video file> folder <folder names with the videos> 

   e.g. 
   vid2tif.exe wmv folder d:\heartbeat

   if all video files are located at d:\heartbeat 

   The result are subfolders "C-1" - "C-4" including tif-images for single time frames. 
 

2. Computes the heartbeat for the extracted images
   for heart frequency segmentation for video C_1 using standard parameters

   heartbeat video d:\heartbeat\C-1 

   In addition, you can specify various parameters, e.g.

   - Use only 16 frames for segmentation and 32 to calculate the frequency:
 
     heartbeat video d:\heartbeat\C-1 min

   - Save segmented region over each original image:

     heartbeat video d:\heartbeat\C-1 yes
   
   - Specify the number of frames used for the heart segmentation (default value 16), e.g. 10    

     heartbeat video d:\heartbeat\C-1 FramesForSeg 20

   - Specify the number of frames used for the frequency calculation (default value 32), e.g. 300                          

     heartbeat video d:\heartbeat\C-1 FramesForFreq 300

   - Segment the heart and calculate the frequency again after VALUE number of frames, e.g. 100

     heartbeat video d:\heartbeat\C-1 update 100
 

   At the end of the video, the threshold for the detection of local maxima can be changed (defualt  value zz =3), a larger value reduces the number of maxima. 
   Finally, the step generates a new folder 

   d:\heartbeat\C-1\results 

   including the following files: 
   1.png             - Detected heart region
   info.csv          - Detected movement in single frames
   Freq*.tiff        - Time series with detected movement in heart region ('*' marks local extrema)
   heartbeat.csv     - Detected heart beats

Contact: 
christian.pylatiuk@kit.edu 
ralf.mikut@kit.edu