Developper
Bio Image Analyst
Type
Description

SliceMap

Whole brain tissue slices are commonly used in neurobiological research for analyzing pathological features in an anatomically defined manner. However, since many pathologies are expressed in specific regions of the brain, it is necessary to have an annotation of the regions in the brain slices. Such an annotation can be done by manual delineation, as done most often, or by an automated region annotation tool.

SliceMap is a FIJI/ImageJ plugin for automated brain region annotation of fluorescent brain slices. The plugin uses a reference library of pre-annotated brain slices (the brain region templates) to annotate brain regions of unknown samples. To perform the region annotation, SliceMap registers the reference slices to the sample slice (using elastic registration plugin BUnwarpJ) and uses the resulting image transformations to morph the template regions towards the anatomical brain regions of the sample. The resulting brain regions are saved as FIJI/ImageJ ROI’s (Regions Of Interest) as a single zip-file for each sample slice.

More information can also be found in "SliceMap: an algorithm for automated brain region annotation", Michaël Barbier, Astrid Bottelbergs, Rony Nuydens, Andreas Ebneth, Winnok H De Vos, Bioinformatics, btx658, https://doi.org/10.1093/bioinformatics/btx658

Execution Platform
Illustrative Image
Supported image dimension
License/Openness
has interaction level
has programming language
has author
Barbier Michaël
Bottelbergs Astrid
Nuydens Rony
Ebneth Andreas
De Vos Winnok H.
has license
MIT
has implementation