zheight

A utility for displaying a 2D contour map of the z-height of a tissue cut

Installation

Install Python 3

Install zheight in its virtual environment (only needs to be done once) ("/path/to" below can be any directory)

python -m venv /path/to/zheight 
pip3 install https://github.com/chunglabmit/zheight/archive/master.zip#egg=zheight

Activate the environment

source /path/to/zheight/bin/activate

Usage

Example:

zheight --stack /path/to/stack/*.tif --output /path/to/output.png

zheight --stack <stack> \
        --output <image-file> \
        [--sigma <sigma>] \
        [--multiplier <multiplier>] \
        [--min-threshold <min-threshold>]

where

<stack> is the glob expression for the stack of tif files to be analyzed. These should be in alphabetical order by z-height, e.g. "img0001.tif" instead of "img0.tif".
<output> the name of the output image. Supported types are probably .png, .jpg and maybe .pdf
<sigma> the smoothing sigma for blurring the image. The default is 20, numbers between 10 and 40 should be pretty good choices.
<multiplier> after computing the otsu automatic global threshold, zheight multiplies the automatic threshold by this factor to get the threshold used by the algorithm. The default is .8 which was arrived at empirically.
<min-threshold> is a minimum threshold that is used if the method above calculates a threshold that is too low.