Anatomical Flatmap Resources

Flatmap resources

Mapmaker

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SCKAN

ApiNATOMY

Map-tools

Flatmap sources

base diagram for ac flatmap and anatomical diagrams: These are the manually-drawn cartoons which provide the base diagram for each species’ flatmap. They are archived in Physiome Project (PMR) as SVG images (e.g., rat flatmap sources). The SVG is annotated with the anatomical terminology used in SCKAN.

SVG File

JSON Files

Examples

MAP tools for Connectivity Knowledge

The map knowledge package provides a Python wrapper for flatmap-related SCKAN queries, and an additional package, map tools, allows SCKAN connectivity to be viewed and explored in a Jupyter notebook.

Physiome Model Repository (PMR)

The source files used in the generation of the flatmaps displayed on the SPARC Portal are stored in version controlled workspaces in the Physiome Model Repository (PMR). See the workspace for the rat flatmap for an example. These source files are used by the Flatmap Maker tools to produce the interactive flatmaps available on the SPARC Portal. Learn more from the PMR User Documentation

Organ Scaffolds

Learn more about Organ Scaffold Maps.

The process for mapping SPARC data to the organ scaffolds is described in some detail in The SPARC DRC: Building a resource for the autonomic nervous system community, so here we focus on enabling the reuse of the organ scaffolds themselves, as well as specific instances of the scaffolds in a given scaffold map.

Documentation for the scaffold mapping tools is available from ABI-Mapping-Tools. The following are quick links to the specific tools used in the SPARC default organ scaffolds workflow:

• Scaffold Creator (for the creation of organ scaffolds)

• Argon Viewer (for the visualization of organ scaffolds)

• Argon Scene Exporter (for exporting the organ scaffolds for interactive exploration on the web, and reuse by other softwares in VTK and STL formats)

Generic organ scaffolds

Quarterly releases of the generic organ scaffolds are published to the SPARC Portal as Anatomical Models. In the same manner as the source flatmap anatomical diagrams, the source of these generic scaffolds are archived in PMR and then published to the SPARC Portal in a manner aimed at supporting reuse.

When a generic scaffold is archived in PMR a provenance record is stored in the archive that explicitly states the version of the software used. The provenance record can be used to recreate the environment that the archived data was created with. With the software environment and inputs to the workflow we can reproduce the data published to the SPARC Portal locally.

Generic organ scaffolds are typically exported in reusable STL and VTK formats. These formats are generated with the SPARC default organ scaffolds workflow and they can be found and downloaded directly from the derivative folder of generic organ scaffold datasets. If the dataset lacks STL or VTK files, the missing files can be generated by following the steps given below.

Creating your own Anatomical Scaffold

To generate anatomical scaffolds, you will need to install the Scaffold Mapping Tools on your local machine.

Documentation for the scaffold mapping tools is available from ABI-Mapping-Tools. The following are quick links to the specific tools used in the SPARC default organ scaffolds workflow:

• Scaffold Creator (for the creation of organ scaffolds)

• Argon Viewer (for the visualization of organ scaffolds)

• Argon Scene Exporter (for exporting the organ scaffolds for interactive exploration on the web, and reuse by other softwares in VTK and STL formats)

Detailed information about the variants, coordinates, and annotations used for each specific organ scaffold can be found in the documentation for the scaffoldmaker library.

Flatmaps

https://docs.sparc.science/v1.0/update/docs/documentation-examples-and-software-for-map-reuse#/

MAP Client

https://sparc.science/tools-and-resources/1mv8q3JckdpSYpPK9dvdKx

Anatomical diagrams

These are the manually-drawn cartoons which provide the base diagram for each species’ flatmap. They are archived in PMR as SVG images (e.g., rat flatmap sources). The SVG is annotated with the anatomical terminology used in SCKAN.

Map maker (Flatmap maker)

Map maker’s source code is hosted on GitHub, which is where issues and feature requests can be raised, and documentation can be found here.

Connectivity knowledge from SCKAN is used to identify which segments of a pre-drawn (but hidden) nerve network that the path of each neuron population group traverses. These paths are then ordered within each nerve segment to minimize the number of crossings between paths, and drawn using an offset from the segment’s centreline.

Releases are versioned in GitHub.

Flatmap server

The flatmap server’s source code is hosted on Github, which is where issues and feature requests can be raised and flatmap server documentation can be found here.

PMR’s Exposure Creation Wizard (see Publishing a Flatmap as a SPARC Dataset).

Databases

The map knowledge package provides a Python wrapper for flatmap-related SCKAN queries, and an additional package, map tools, allows SCKAN connectivity to be viewed and explored in a Jupyter notebook.

Measuring reuse

Beyond the tracking of dataset reuse (downloads, citations, etc.) already handled by the SPARC Portal, we will look to track all routes of reuse of the maps and supporting software. At a minimum, this will include tracking download or reuse of the open-source codes via Github and addition of maps to SPARC data that is not completed by MAP-Core. Tracking statistics for map research product reuse will be aggregated and made available to NIH.

A preliminary page has been set up to present map reuse statistics pulled from the Github repositories used for the mapping tools and dependent codes. This page dynamically updates with current data on page load. We will continue to add software information and additional statistics as they become available and will ensure the scaffold mapping SOP is updated to ensure new scaffold maps are able to be tracked in a similar manner.