crop-xml.md

Cropping xml file

To "crop" an xml file, i.e. only include cell coordinates corresponding to given anatomical areas.

    cellfinder_xml_crop --xml-dir xml_directory --structures-file chosen_structures.csv --registered-atlas registered_atlas.nii --hemispheres hemispheres.nii

Arguments

Run cellfinder_xml_crop -h to see all options.

Mandatory

• --xml-dir Directory containing xml files to be cropped
• --structures-file Curated csv structure list (as per the allen brain atlas csv)
• --registered-atlas The path to the atlas registered to the sample brain
• --hemispheres The atlas with just the hemispheres encoded

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

The following options may also need to be used:

• --hemisphere-query Which hemisphere to keep (1 or 2). Default: 0 (all)

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