macro:tiled_autofocus_hyperstack
// Tiled autofocus hyperstack macro // Breaks down the image into ROIs of user defined size // Selects the in focus slice for each ROI (in each frame of the hyperstack) and creates a new stack // of montaged in-focus ROIs for each frame // Based on algorithm F-11 "Normalized Variance" // In: Sun et al., 2004. MICROSCOPY RESEARCH AND TECHNIQUE 65, 139–149. // And the original macro by Andy Weller http://imagejdocu.tudor.lu/doku.php?id=macro:normalized_variance //Get image details type = bitDepth(); if (type==8) {type="8-bit";} else {if(type==16) {type="16-bit";} else{if(type==32) {type="32-bit";} else {if(type==24) {type="RGB";}}}} StackID=getTitle(); Stack.getDimensions(width, height, channels, slices, frames); //Check its in the correct format if (channels>1) {exit("The hyperstack has 2-channels please reduce dimensionality")} else{} if (channels==frames) {exit("The stack does not contain multiple z-positions")} else{} //Prompt for divider Dialog.create("Select number of tiles"); Dialog.addMessage("The number of tiles must be divisible by 4"); Dialog.addNumber("Tile number:", 4); Dialog.show(); tiles = Dialog.getNumber(); //Divide image into non-overlapping ROIs roiManager("reset"); run("Select None"); Stack.getDimensions(width, height, channels, slices, frames); //note the divider must be a multiple of 4!!!!!!!!! x = 0; y = 0; width = width/tiles; height = height/tiles; spacing = 0; numRow = tiles; numCol = tiles; for(i = 0; i < numRow; i++) { for(j = 0; j < numCol; j++) { xOffset = j * (width); yOffset = i * (height); makeRectangle(x + xOffset, y + yOffset, width, height); roiManager("Add"); } } roiManager("Show All"); number_ROI = roiManager("count"); setBatchMode(true); //Work through the ROI set and pick the most infocus slice for each ROI for (k=1; k<=frames; k++) { Stack.setFrame(k); for (z=0; z<number_ROI; z++){ normVar = 0; normVar1 = 0; m=0; mean=0; stdev=0; for (l=1; l<=slices; l++){ selectWindow(StackID); run("Select None"); roiManager("Select", z); Stack.setFrame(k); Stack.setSlice(l); getStatistics(area, mean, min, max, std, histogram); normVar = std*std/mean; if (normVar>normVar1) { m = l; normVar1=normVar;} else {normVar1 = normVar1;} } //Build a new stack of the in-focus tiles at each timepoint selectWindow(StackID); run("Select None"); roiManager("Select", z); Stack.setFrame(k); Stack.setSlice(m); run("Copy"); if (isOpen(StackID+"_Focused")){ selectWindow(StackID+"_Focused"); if (z==0) {run("Add Slice");} } else{ newImage(StackID+"_Focused", type, 512, 512, 1); } run("Restore Selection"); run("Paste"); selectWindow(StackID); Stack.setSlice(l); } } selectWindow("ROI Manager"); run("Close"); setBatchMode("exit and display"); //Versions: // 0.1 15/08/2013 // 0.2 16/07/2014 - fixed bug in line 77 //Richard Mort 27/09/2018
macro/tiled_autofocus_hyperstack.txt · Last modified: 2019/04/12 13:13 by 127.0.0.1