Whisker tracking

A description of this software as well as detailed instructions and a tutorial may be found here.

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Downloading

Pre-built binaries are available for download.

See the instructions for building below.

Tip: Git on Windows

1. Install msysgit.

2. You may need to run the following command so that the https protocol will work correctly

   git config --global http.sslcainfo "/c/Program Files (x86)/Git/bin/curl-ca-bundle.crt"
   

3. Clone the repository

   git clone https://github.com/nclack/whisk.git
   

Building

This package uses a Cmake based build system. The basic build steps are similar under Windows, OS X, and Linux. On a unix-y system, the procedure looks like this:

1. Install CMake 2.8 or better.

2. Install bison if it's not already available on your system.

   For windows, use GnuWin32 Bison. It's best to install it to a path that lacks spaces such as "C:\gnuwin32".

3. Install awk.

   For windows, use GnuWin32 Gawk.

4. On Windows and OS X, you'll have to install developer tools. On Windows, that's Visual Studio; one of the free "Express Edition" versions is fine. On OS X, install the XCode developer tools.

   If you plan on building a binary redistributable on windows, you may also want to install the Nullsoft Scriptable Install System.

5. Start in the root of the source directory (in a terminal). The contents of this directory look something like this:

    3rdParty/
    CMakeLists.txt
    LICENSE.txt
    README.txt
    TODO
    build/
    config.h.in
    docs/
    include/
    matlab/
    oldbuild/
    pipeline/
    python/
    src/
    ui/
   

6. Type these commands:

    mkdir build
    cd build
    cmake ..
    make
   

CMake works by building the Makefile, or other required project files, in the "build" directory you created. You don't have to use a Makefile; XCode projects, Eclipse projects, Visual Studio projects, etc ... can be generated. To generate these other project types replace the "cmake .." step with "cmake-gui ..". The GUI will show available options. See the CMake documentation for more details.

File formats

Whiskers

Whiskers can be stored in either a text or binary format. There is a command line utility, whisker_convert, provided to convert between different supported formats. batch.py can be used to speed up the process of converting many files.

The most detailed description of each format can be found in the corresponding whisker_io_*.c files implimenting the readers/writers for each format.

In general, each whisker segment in a file is comprised of a unique id and a number of data points describing the shape as output from the tracing program.

Measurements

The measurements file stores the features of traced curves used for classification, such as follicle position, angle and whisker length. Additionally, after classification, this file records the determined identity of each traced curve.

Graphical interface

See ui/README for instructions on how to use the graphical user interface.

  ui2.py --help

Changes

v1.0.0 to v1.0.2

• improved FFMpeg support

  • more video formats supported

  • newer version of FFMPEG used on windows and 64-bit support added

• change how whiskers were ordered to better support videos imaging both sides of a mouse's face.

• added a special heuristic classifier for tracking single whiskers

• added a special heuristic classifier adapted for tracking whiskers on both sides of a mouse's face.

• added Matlab mex binaries to support reading and writing of measurements files, as well as reading of whiskers files.

• seeding function used to initially find whiskers is now more efficient and provides more accurate estimates of local whisker angle.

• Improved the installer so python and Matlab functionality is better supported.

• added another measurements file format that remembers the face position. The new format is now the default. A warning may be issued for files that use the old format. Run the measurements_convert command to update your files, if necessary.