description
Visualise cell positions at a glance

Heatmap generation

To generate a heatmap of detected cells, which shows cell distributions in a more intuitive way that showing individual cell positions:

Usage

{% hint style="warning" %} This tool is a work in progress, and the usage may change {% endhint %}

    heatmap cell_classification.xml heatmap.nii raw_data registered_atlas.nii -x 2 -y 2 -z 5

Run heatmap -h to see all options.

cellfinder classified cells file (usually cell_classification.xml)
Output filename. Should end with '.nii'. If the containing directory doesn't exist, it will be created.
Path to raw data (just a single channel). Used to find the shape of the raw image that the detected cell positions are defined in.
Registered atlas file from amap (typically run automatically in cellfinder). File is usually registered_atlas.nii.

{% hint style="warning" %} You must also specify the pixel sizes, see Specifying pixel size {% endhint %}

--heatmap-bin Heatmap bin size (um of each edge of histogram cube)
--heatmap-smoothing Gaussian smoothing sigma, in um.
--no-mask-figs Don't mask the figures (removing any areas outside the brain, from e.g. smoothing)