skeleton keys

This package supports the skeletal analysis of morphologies.

We recommend installing this on Linux or Mac via conda. We aren't generally currently supporting Windows, though there are some scripts which may work and be useful on that platform. This is because we are utilized fenics-dolphix which is not available on Windows.

Installation instructions

clone the repo, setup a conda environment with the proper requirements and activate it

git clone git@github.com:AllenInstitute/skeleton_keys.git
cd skeleton_keys
conda env create -f environment.yml
conda activate skeleton_keys_env

pip install skeleton keys

pip install .

Internal Allen Institute Use

In order to download morphologies from the internal LIMS system, you must set certain environment variables to connect properly. These include

    LIMS_HOST
    LIMS_DBNAME
    LIMS_USER
    LIMS_PASSWORD

Contact the technology team if you need to get credential details to access LIMS.

Scripts

After installation the following console scripts will be available to run from the command line of your environment. To see detailed instructions on each script type the name of the SCRIPT_NAME --help

skelekeys-layer-aligned-swc

script to take a swc file, a polygon definition (representing cortical layers and pia/wm surfaces), a common layer cortical boundary file and produce a swc file that has been remapped to common layer boundaries.

skelekeys-profiles-from-swcs

script to take a directory of layer-aligned swc files, a common layer boundary file and return layer histogram file and a soma depth file for the cells

skelekeys-morph-features

script to take a list of upright cells, a layer histogram file, and a soma depth file, and extract morphological features from those cells in a long format.

This script can be run without upright cells, and/or a layer histogram file, and/or a soma depth file. Just pass in the swc files that you would like to quantify and leave the histogram and soma depth file arguments as the default (None).

skelekeys-postprocess-features

script to take a long form set of features and post-process them to remove zeros and perform zscoring and/or uniform scaling of features.

Statement of Support

This code is an important part of the internal Allen Institute code base and we are actively using and maintaining it. Issues are encouraged, but because this tool is so central to our mission pull requests might not be accepted if they conflict with our existing plans.