macro "Cell Viewer" { versionFIJI = "1.53b"; requires(versionFIJI); // Title Pop Up showMessage("Pomegranate Cell Isolator Tool", "" +"
Pomegranate
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Cell Isolator Tool
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" +"
Virginia Tech, Blacksburg, Virginia
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Department of Biological Sciences - Hauf Lab
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    " +"
  • FIJI Version Required: " + versionFIJI +"
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Please read accompanying documentation
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[Erod Keaton Baybay - erodb@vt.edu]
"); showMessageWithCancel("Prerun Cleanup","This macro performs a prerun clean up\nThis will close all currently open images without saving\nClick OK to Continue"); cleanAll(); // Designate Input Image Dialog.create("Input Image"); Dialog.addChoice("Input Method", newArray("Select Image from Directory","Manually Enter Path")); Dialog.show(); if (Dialog.getChoice() == "Select Image from Directory") imagePath = File.openDialog("Choose an Input File"); else imagePath = getString("Image Path", "/Users/hauflab/Documents"); open(imagePath); call("ij3d.ImageJ3DViewer.close"); getVoxelSize(vxy, vxy, vz, unit); original = getTitle(); close("\\Others"); run("Select None"); roiManager("Reset"); print("\\Clear"); setSlice(round(nSlices/2)); run("Duplicate...", "title=TEMP duplicate"); run("Z Project...", "projection=[Max Intensity]"); close("TEMP"); setTool("Wand"); waitForUser("Select a cell (Wand Tool)"); if (selectionType() != -1) { roiManager("Add"); selectImage(original); roiManager("Select", 0); run("Duplicate...", "title=Extracted_Cell duplicate"); setBackgroundColor(0, 0, 0); run("Clear Outside", "stack"); run("Select None"); roiManager("Reset"); close("MAX_TEMP"); run("8-bit"); setThreshold(3, 255); setOption("BlackBackground", true); run("Convert to Mask", "method=Default background=Dark black"); roiManager("Deselect"); run("Select None"); run("Canvas Size...", "width=" + (getWidth() + 20) + " height=" + (getHeight() + 20) + " position=Center zero"); // Medial Axis Transform for Size Measurement selectImage("Extracted_Cell"); run("Z Project...", "projection=[Max Intensity]"); rename("TEMP"); run("Duplicate...", "duplicate title=Skeleton"); run("Skeletonize", "stack"); run("Select All"); skeleLength = (getValue("RawIntDen")/255) * vxy; selectImage("TEMP"); run("Duplicate...", "duplicate title=Distance_Map"); run("Distance Map", "stack"); imageCalculator("AND create stack", "Distance_Map","Skeleton"); rename("MAT"); close("Skeleton"); close("Distance_Map"); close("TEMP"); // 0 to NaN run("32-bit"); run("Reciprocal"); run("Reciprocal"); run("Select All"); Rwidth = getValue("Mean") * vxy; Rlength = skeleLength + (2 * Rwidth); close("MAT"); showOverlay = getBoolean("Show Ideal Reconstruction Comparison?"); run("Analyze Particles...", "exclude clear add stack"); roiManager("Select", Array.getSequence(roiManager("Count"))); roiManager("Combine"); Elength = getValue("Major") / vxy; Ewidth = getValue("Minor") / vxy; Eangle = getValue("Angle"); Flength = getValue("Feret") / vxy; Fwidth = getValue("MinFeret") / vxy; Fangle = getValue("FeretAngle"); if (showOverlay) { // Ellipsoidal Overlay run("Rotate...", "rotate angle="+(Eangle)); getSelectionBounds(rx, ry, bx, by); shiftx = round(Elength - bx)/2; shifty = round(Ewidth - by)/2; makeRectangle(rx - shiftx, ry - shifty, Elength, Ewidth, Ewidth); run("Rotate...", " angle="+(-Eangle)); Roi.setStrokeWidth(1); Roi.setStrokeColor("red"); Overlay.addSelection; run("Select None"); roiManager("Select", Array.getSequence(roiManager("Count"))); roiManager("Combine"); // Feret Overlay run("Rotate...", "rotate angle="+(Fangle)); getSelectionBounds(rx, ry, bx, by); shiftx = round(Flength - bx)/2; shifty = round(Fwidth - by)/2; makeRectangle(rx - shiftx, ry - shifty, Flength, Fwidth, Fwidth); run("Rotate...", "rotate angle="+(-Fangle)); Roi.setStrokeWidth(1); Roi.setStrokeColor("yellow"); Overlay.addSelection; Overlay.show; } print("[Size Information]"); print("Feret Length: " + (Flength * vxy) + " " + unit); print("Feret Width: " + (Fwidth * vxy) + " " + unit); print("Reconstruction Length: " + Rlength + " " + unit); print("Reconstruction Width: " + 2 * Rwidth + " " + unit); setSlice(round(nSlices/2)); roiManager("Show None"); run("Select None"); roiManager("Deselect"); run("3D Viewer"); call("ij3d.ImageJ3DViewer.setCoordinateSystem", "false"); call("ij3d.ImageJ3DViewer.add", "Extracted_Cell", "None", "Extracted_Cell", "0", "true", "true", "true", "1", "0"); call("ij3d.ImageJ3DViewer.select", "Extracted_Cell"); call("ij3d.ImageJ3DViewer.setColor", "255", "255", "255"); selectWindow("Log"); waitForUser("Cell Isolated!"); } }