GraphML Importer

  • Menu Location: File > Import > Import GraphML

  • Description:

    • Imports the data stored in the specified GraphML file into the project.

    • Allows importing spots that have been tracked outside Mastodon

    • Spots have to be saved in a GraphML file with a specific format

    • Besides the spots, also links, labels, track_ids and features can be imported

    • The X, Y, Z coordinates are scaled by the pixel sizes read from the setup with the specified id.

  • Command name: import graphml

  • Default bindings: Not mapped

  • Artifact: mastodon

  • Distribution: Included in the Mastodon update site.

  • Link to code: https://github.com/mastodon-sc/mastodon/tree/master/src/main/java/org/mastodon/mamut/io/importer/graphml

  • The dialog: graphml_import.png

GraphML format requirements

  • The GraphML file must contain keys for properties with attr.name ‘x’, ‘y’, ‘z’ and ‘frame’ to be properly imported.

  • If it contains the key with attr.name ‘label’, data with this key is imported as spot labels.

  • Other property keys are imported as projections in a new feature.

  • Right now, only properties declared for nodes are imported this way.

  • The properties are imported in Mastodon with no dimension.

Example

  • Demo data:

    • graph_t0_t4.graphml

    • pos1_t1-5_cropped_H2B.xml and pos1_t1-5_cropped_H2B.h5

    • Data from Hiromune Eto and Jan-Daniël de Leede from the Sonnen lab, Hubrecht Institute, Netherlands, shared with permission. The image is a 3D timelapse of a mouse intestinal organoid grown as an epithelial monolayer, expressing H2B-mCherry. The data was generated by Hiromune Eto. This example contains only the first 5 timeframes