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Contents

Concepts

Command line interface

The programs described below are run from your operating system's command line; they are not Matlab functions. Typically, each program reads a file as input and outputs the results to another file. These output files may be read by Python or Matlab functions provided by this package.

More information on the command line for your operating system may be found:

Interchangeable parts

There are four command line program to trace and track whiskers in a movie. Each of these programs represents a different step in the tracking procedure. By keeping these steps separated, rather then glomming everything into a single command, one can swap out any of these steps with a customized tool.

The most useful example of this is the classify step. This step uses a few heuristic rules to give a first guess as to whether a traced object is part of a whisker or not. These rules might change form experiment to experiment. By replacing the classify program with your own Matlab script, for example, one can customize this step but still take advantage of other parts of the Whisker Tracking package.

Tracing

Videos are automatically analyzed to estimate backbone positions (with subpixel precision) for segments of whiskers, facial hairs, and other dark line-line objects. We try to take an approach favoring false positives; it is better to trace too many things than to fail to detect the presence of a whisker.

Each frame of a video is treated independently. Subsequent steps will try to assign labels to traced segments identifying which segments belong to which whisker.

Measurement

Rather than compare the point-by-point representation of the backbone of a traced segment, a set of features descriptive of the shape are used for comparison.


Table 1: Features

feature

description

time

The index of the frame in the video on which the traced segment was found.

length

Length of the traced path in pixels.

tracing score

Tracing involves finding the optimal correlation between a parameterized filter and the image at a point. This optimal value is a score. This is the median of these scores evaluated at points along a traced segment.

angle at follicle

Degrees of deflection away from the animal's left-right axis.

mean curvature

The average curvature over the traced path in units of `1/pixel`.

follicle position

(x,y) point in pixels.

tip position

(x,y) point in pixels.

Classification

Two steps are used to identify which segements belong to which whiskers throughout a video uses two steps. A first guess is made that separates segments belonging to whiskers from other traced segments. This first guess is used to generate statistics based on measured features. These statistics are used in a second pass, together with the idea that whiskers maintain an order along the face, in order to refine the guess and assign specific identities for different imaged whiskers.

Reference

Note

These programs require special files to be present in the current working directory.

trace

Performs fully automated detection and tracing of all whiskers.

Usage

  trace <video> <destination.whiskers>

Parameters

<video>

The path to the video file. The video must be one of the following formats:

<destination.whiskers>

The path to the file to which results will be saved.

Example

  trace path/to/data/movie.mp4 path/to/data/result.whiskers

measure

Measures several properties of the traced segments output from #trace. Outputs a table with an entry for each traced segment and fields for the features listed in the features table.

Usage

  measure --help
  measure --face <side>         <source.whiskers> <destination.measurements>
  measure --face <x> <y> <axis> <source.whiskers> <destination.measurements>

Parameters

-h, --help

Displays a help message.

--face <side>, --face <x> <y> <axis>

<side> may be left, right, top, or bottom.

Indicates the side of the image along which the face is oriented. The value effects how follicle and tip position are estimated.

<side> is used for videos recorded in such a way that the mouse face lies on one side of the image with the whiskers protruding into the field. Using <side> may not work well if the face is not confined to one side of the image or when the whisker pad is located near a corner of the image.

When <side> doesn't work well, use <x> and <y> should be the approximate coordinates of the center of the whisker pad. <axis> should be x or h if the face (the anterior-posterior axis) lies mostly in along the image's horizontal axis. Otherwise, <axis> should be y or v to indicate the vertical axis.

<source.whiskers>

The source file containing the traced whisker shapes.

<destination.measurements>

The destination file containing the table of computed features. This file will also be used to keep track of whisker identities in later steps.

Examples

  measure --face left path/to/data/result.whiskers path/to/data/result.measurements

  measure --face 30 420 x path/to/data/result.whiskers path/to/data/result.measurements

classify

Uses a length threshold to seperate whisker segments from other traced segments (e.g. facial hairs). Looks for frames with the expected number of long segments and provides a preliminary label according to their order on the face.

Usage

  classify --help
  classify <source.measurements> <destination.measurements> <side>         --px2mm <double> -n <int> [--limit<low>:<high>] [--follicle <int>]
  classify <source.measurements> <destination.measurements> <x> <y> <axis> --px2mm <double> -n <int> [--limit<low>:<high>] [--follicle <int>]

Parameters

-h, --help

Displays a help message.

<side>, <x> <y> <axis>

<side> may be left, right, top, or bottom.

Indicates the side of the image along which the face is oriented. The value effects how follicle and tip position are estimated.

<side> is used for videos recorded in such a way that the mouse face lies on one side of the image with the whiskers protruding into the field. Using <side> may not work well if the face is not confined to one side of the image or when the whisker pad is located near a corner of the image.

When <side> doesn't work well, use <x> and <y> should be the approximate coordinates of the center of the whisker pad. <axis> should be x or h if the face (the anterior-posterior axis) lies mostly in along the image's horizontal axis. Otherwise, <axis> should be y or v to indicate the vertical axis.

<source.measurements>

The source file containing measured features of traced segments.

<destination.measurements>

The destination file. This may be the same as <source.measurements>. Contains the table of measurements in <source.measurements> with updated assigned identities.

--px2mm <double>

The pixel size in millimeters. Should be in units of mm/px.

-n <int>

The number of segments longer than the length threshold expected in most frames. Typically, this is the number of imaged whiskers.

If set to -1, #classify will choose the minimum length threshold that maximizes the number of frames with the same number of long segments.

--limit<low>:<high>

Optional.

#classify adaptively finds the a minimum length threshold that yields the most number of frames with long whiskers. Use <low> and <high> to bound the length threshold. These should have in units of mm.

--follicle <int>

Optional.

Only count follicles that lie on one side of the line specified by this threshold (in pixels). The direction of the line points along the x or y axis depending which is closer to the orientation of the mouse's face.

Example

Run classify for a video with the face on the left of the image with a pixel size of 40 µm. Label a segment as a whisker if the segment is longer than a threshold between 1 mm and 50.0 mm and if the follicle is found on the left of the vertical line: x=100 px. Automatically try to determine the number of
whiskers.

  classify source.measurements destination.measurements left --px2mm 0.04 -n -1 --limit1.0:50.0 --follicle 100

reclassify

Refines an initial guess of segment identities.

Usage

  reclassify --help
  reclassify -n <int> <source.measurements> <destination.measurements>

Parameters

-h, --help

Displays a help message.

<source.measurements>

The source file containing measured features of traced segments with initial guess's for segment identities.

<destination.measurements>

The destination file. This may be the same as <source.measurements>. Contains the table of measurements in <source.measurements> with updated assigned identities.

-n <int>

The number of whiskers imaged. Typically, this is the same number used for #classify -n <int>.

If set to -1, #reclassify will use the guess provided by <source.measurements>.

Example

  reclassify -n 3 source.measurements destination.measurements

whisker_convert

Converts between different formats available for measurements files. This utility is mainly used for updating to newer file formats.

It can also be used to convert files to a "human readable" text format.

Usage

  whisker_convert -h
  whisker_convert <source.whiskers> <destination.whiskers> <format>

Parameters

-h, -help

Displays a help message.

<source.whiskers>

The source whiskers file.

<destination.whiskers>

The destination file. This may be the same as <source.whiskers>, in which case the original will be overwritten.

<format>

The destination format to use. To get a list of available formats see:

    whisker_convert -h
Warning

The whiskpoly1 format is a lossy format and may not retain interesting aspects of traced whiskers such as the angle near the follicle. Don't use it.

Example

  whisker_convert source.measurements destination.measurements whiskbin1

measurements_convert

Converts between different formats available for measurements files. This utility is mainly used for updating to newer file formats and converting to "human readable" text.

Usage

  measurements_convert -h
  measurements_convert -<source.measurements> <destination.measurements> <format>

Parameters

-h, -help

Displays a help message.

<source.measurements>

The source measurements file.

<destination.measurements>

The destination file. This may be the same as <source.measurements> in which case the original will be overwritten.

<format>

The destination format to use. To get a list of available formats see:

    measurements_convert -h

Example

  measurements_convert source.measurements destination.measurements v1

report

Compares two .measurements files and prints a report of differences in identity assignments between whiskers.

Usage

  report (-diff|-hist) <A.measurements> <B.measurements>

Parameters

-diff

Lists the frames where differences were discovered.

-hist

Histograms the number of differences per frame.

<A.measurements>, <B.measurements>

The two measurements files to compare. The same set of whiskers should be labelled in both. The labels used to identify
trajectories do not have to be the same; report will find the most likely correspondence given the curve features
recorded in the .measurements files.

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