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plugin:segmentation:jslic:start [2019/04/12 13:13] (current)
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 +====== 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.
plugin/segmentation/jslic/start.txt ยท Last modified: 2019/04/12 13:13 (external edit)