Created
June 17, 2025 11:18
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show that different thresholds can output similar results
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| // clear the environment | |
| run("Close All"); | |
| roiManager("Reset"); | |
| //open an image | |
| run("Fly Brain (1MB)"); | |
| // make it composite, duplicate one slice and get information | |
| run("Make Composite"); | |
| run("Duplicate...", "duplicate channels=1 slices=27"); | |
| getDimensions(width, height, channels, slices, frames); | |
| // here we run the Auto_Threshold | |
| run("Auto Threshold", "method=[Try all] white"); | |
| getDimensions(output_Width, output_Height, output_channels, output_slices,output_frames); | |
| // I will highlith the categories with some ROIs of different colors | |
| xSize = 258; | |
| ySize = 274; | |
| // so I define the categories and their colors | |
| //arrayCatNbr = newArray(1,2,3,1, 2,1,1,3 ,1,2,1,2 ,1,2,2,1); | |
| //Mod from 2018/06/12 to account for new auto threshold method | |
| arrayCatNbr = newArray(1,2,2,1, 1,2,1,2,2,3,1,1,2,1,3,2,1); | |
| arrayRoiColor = newArray("50FFFF00", "5000FF00", "50FF00FF"); | |
| // adding ROIs | |
| i = 0; | |
| for (y = 0 ; y < output_Height ; y+=ySize){ | |
| for (x = 0 ; x < output_Width ; x+=xSize){ | |
| if(i<lengthOf(arrayCatNbr)) { | |
| makeRectangle(x, y, xSize, ySize); | |
| Roi.setName("Cat-"+arrayCatNbr[i]); | |
| Roi.setFillColor(arrayRoiColor[arrayCatNbr[i]-1]); | |
| roiManager("Add"); | |
| i++; | |
| } | |
| } | |
| } | |
| // Sort the ROi and Tile the images | |
| roiManager("Sort"); | |
| run("Tile"); | |
| selectImage("Montage") | |
| roiManager("Show All"); |
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