ColSeg ImageJ Plug-in User Manual
Contents
1. un e Press the Process button to segment the image The pixels inside the image ROI are assigned to any of the three classes according to similarity to their representative pixels in the LAB color space e The total area for each class the number of segments is shovvn in the Result box The statistics can be exported as a text file E Color Segmentation Setting Sampling size CA Color 8 intensity a Select Color Red i Green segments Roundness Average area Backg d 1 Morphology pixels _ den Area _ Fill holes Background Area _ Split cells Size Roundness Max relative cut2. ColSeg ImageJ Plug in User Manual Brief description This is a custom software for color image segmentation that was implemented as an ImageJ plug in In ImageJ the user opens an image of the entire wound region The software categorize all pixels into one of three colors namely green red and white The user chooses up to 5 representative pixels within an image to train the software to recognize the color selected A region of interest ROI can be selected using the Polygon Selection to spatially restrict image processing Without ROI selection pixel categorization is applied to the whole image During processing the image is transformed from the RGB into the CIELAB color space which was designed to provide a better approximation of human color perception than RGB Each pixel in the ROI is assigned a class label green red or background based on similarity to the mean color of the sampled pixels in the CIELAB color space Lastly the software identify connected pixels with the same class as a segment The Result panel displays the statistical analysis of the image segmentation including total number of pixels of each of the three colors and number and average size of the segments To ensure reproducibility the parameters for color selection was saved and reused for other images Prerequisites e Download and install ImageJ or FIJI on your computer system e Make sure that the Gray Morphology jar plugin file is present in the plug
3. ins folder If not download from http rsbweb nih gov ij plugins morphology html e Download the colseg jar file from the following URL http web bii a star edu sg archive colseg and install in the ImageJ plugins folder Color Image Segmentation e Open ImageJ e Open stitched color image e Open ColSeg using Menu gt Plugins gt ColSeg S Color Segmentation Setting Sampling size 0 Color amp intensity La ae Process Result Unit in pixel 4 Foreground 1 Foreground 1 LJ Foreground 2 O Background 1 Area segments Ll Background 2 TE Foreground 2 Area segments Roundness Average area Morphology pixels Background 1 Area _ Fill holes Background 2 Area Merge foregrounds al Export C Split cells Size gt 200 Roundness l0 5 Max relative cut 0 4 e In the Select Color box choose one of the color classes for which define representative pixels by clicking on CheckBox blue arrow Here we assume that the user needs to distinguish between three classes of pixels two foreground red and green and one background class It is possible to change the names of the labels e Inside the color image select up to 5 representative points which will be shown in a separate dialog below Repeat this step for all classes of pixels e Color selection profiles can be saved and loaded for the segmentation of other images Color selected so far o gt
Download Pdf Manuals
Related Search