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
SliceMap is a FIJI (ImageJ) plugin. Fiji can be downloaded from www.fiji.sc.
The example dataset with 60 downscaled brain slices and brain region annotations can be found in the dataset subfolder
To install the SliceMap plugin, there are two options:
- Either copy the jar-file SliceMap_-1.0-SNAPSHOT-jar-with-dependencies.jar (this is a fat jar, including its own version of ImageJ and necessary libraries) into the plugins folder of the ImageJ/FIJI application (typically this folder is …/Fiji.app/plugins/)
- or copy the the jar-file SliceMap_-1.0-SNAPSHOT.jar into the plugins folder and unzip the file SliceMapLibs.zip (the necessary dependencies not included in FIJI) into the jars folder of the ImageJ/FIJI application (typically this folder is …/Fiji.app/jars/). This second method avoids possible collisions between existing libraries in FIJI and SliceMaps dependencies.
The plugin can then be called from Plugins > SliceMap > SliceMap.
To use SliceMap directly one can also just start it (by e.g. double clicking it, this works only for the SliceMap_-1.0-SNAPSHOT-jar-with-dependencies.jar file), this way it will open its own ImageJ instance to run in.
Further explaination of the usage and input/output of the SliceMap plugin is given in the user_manual.pdf file.
Michael Barbier and Winnok De Vos
This project is licensed under the MIT License - see the LICENSE.md file for details