Map-Tools

Overview

Map-tools is a jupyter notebook package that provides information on individual neuron connections, according to the knowledge in SCKAN. It can be used to understand each connection and the respective anatomical features involved.

Source Code

https://github.com/AnatomicMaps/map-tools

Installation

Map-tools is best run under a python environment and is reliant on Poetry. Map-tools can then be installed by cloning the GitHub repository.

$ git clone https://github.com/AnatomicMaps/map-tools

Having installed Poetry via the official installer instructions, clone and enter the map-tools directory. Install a Poetry environment with

$ poetry install

Usage

Once installed, map-tools can be run by opening Jupyter Notebook. In the map-tools directory, run jupyter notebook via poetry.

$ poetry run jupyter notebook

The command will provide access to the notebook with a URL, which should then be pasted into a browser window.

Once opened, navigate to and open the connectivity_graph.ipynb notebook in the connectivity-graph folder. A valid SCICRUNCH Key must be input in order to draw knowledge from SCKAN. This can be done by inserting the key under a scicrunch_key field as shown in Figure 2. Note that a SciCrunch key can be generated by setting up a SciCrunch account.

Neuron paths from ApiNATOMY Models can now be visualised, as seen in Figure 3. The desired neuron path can be visualised by changing the entity field. Table 1 represents the ilxtr attribute for each model. Note that the ID of each path is dependent on the visualisation of paths in each model.

Table 1: ilxtr attributes of each path in the respective ApiNATOMY models. These are used to visualise said paths in the connectivity_graphy.ipynb file.