====== jSLIC - superpixels ======

We made a Java-based open source implementation jSLIC - the superpixel clustering with better performance than the original Simple Linear Iterative Clustering. For more info, please see [[http://fiji.sc/CMP-BIA_tools#jSLIC_-_superpixels|Fiji wiki]]. 

===== How to use the plugin =====

{{ :plugin:segmentation:jslic:fiji_slic_gui.jpg|jSLIC interface}}
As you can see the Interface to the plugin contains a parameters for superpixel configuration and also its final visualisation.

==== Configuration ====

For the configuration there are only two parameters to be set:
  * **Init. grid size** - in general it can be seen as an average superpixels size.
  * **Regularisation** - influence the compactness of estimated superpixels. The range is from 0 (very elastic superpixels) to 1 (superpixels are nearly squares). Experimentally, we set as optimal value 0.2 for most cases.

==== Visualisation ====

To show of handle segmentation results we presented a few approaches:
  * //Overlap contours// - simply draw the contours on resulting superpixels into the image by chosen colour.
  * //Export segments as ROIs// - all superpixels are exported as polygons into the [[http://rsb.info.nih.gov/ij/plugins/roi-manager-tools/index.html| ROI Manager]].
  * //Show final segmentation// - add one more stack and fill each superpixel by a random colour. 
  * //Save segmentation into file// - export the superpixel segmentation into a text file as segmentation matrix with labels.

{{:plugin:segmentation:jslic:human_breast_cytokeratin_jslic.jpg?400 |Sample of jSLIC segmented histological tissue}}
{{ :plugin:segmentation:jslic:human_breast_cytokeratin_jslic_50px_0-2.jpg?400|Sample of jSLIC segmented histological tissue}}

===== References =====
Borovec, J., & Kybic, J. (2014). jSLIC : superpixels in ImageJ. Computer Vision Winter Workshop. Praha.