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Heatmap generation

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

+heatmap

Overlay on raw data and segentation from +amap added separately

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Usage

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

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Run heatmap -h to see all options.

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Positional arguments

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  • Cellfinder +classified cells file (usually cell_classification.xml)

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  • Output filename. Should end with ‘.nii’. If the containing directory doesn’t +exist, it will be created.

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  • 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.

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  • Registered atlas file from amap +(typically run automatically in +Cellfinder). File +is usually registered_atlas.nii.

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Keyword arguments

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  • -x or --x-pixel-size Pixel spacing of the data that the cells are +defined in, in the first dimension, specified in um.

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  • -y or --y-pixel-size Pixel spacing of the data that the cells are +defined in, in the second dimension, specified in um.

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  • -z or --z-pixel-size Pixel spacing of the data that the cells are +defined in, in the third dimension, specified in um.

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The following options may also need to be used:

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  • --heatmap-bin Heatmap bin size (um of each edge of histogram cube)

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  • --heatmap-smoothing Gaussian smoothing sigma, in um.

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  • --no-mask-figs Don’t mask the figures (removing any areas outside the +brain, from e.g. smoothing)

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