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plugin:stacks:toolset_for_manual_extraction_of_best-focused_z-slices_from_hyperstack:start [2019/04/12 13:13] (current)
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 +**Hyper with Stacks**
 +A toolset facilitating manual extraction of focused slices from hyperstacks
 +The following toolset was designed to facilitate manual extraction of in-focus z-slices from 4D and 5D (x,y,z,t,c) sets of timelapse images such as microscopy of cancer cell migration on the chick embryo or mouse. ​ The toolset enables a user to scroll through a 4 or 5D dataset displayed as a hyperstack, Setting the Focus (with the F1 key or by clicking the toolset button), and then split out (F2) of the hyperstack a simple 3D stack (x,y,time) of all the best focus points. ​ Multiple channels can be split out using the index generated by setting the focus. ​ Selecting the most focused z-position for each timepoint is possible but not necessary. ​ The program will use the current z position for all the timepoints inbetween the previous timepoint and current timepoint. ​ A log is printed out that can be saved as a reference.
 +William J Ashby
 +and hopefully others as they make worthwhile contributions to this tool
 +I want to thank the creator/s of the Magic Montage toolset. ​ Before finding [[howto:​working:​work_with_magic_montage|Magic Montage]] I rarely used the toolsets or even realized that I could make them using macro language.
 +The toolset provides buttons to do the following:
 +  - Convert a stack to hyperstack (In order to save time, the default values can be adjusted in the code).
 +  - Set the focus point F1 (i.e. index your z position) for all the timepoints inbetween the previously indexed (or first) timepoint and the current timepoint.
 +  - Split out the currently selected channel from your hyperstack using the index of focused z positions.
 +  - Re-initialize F2, which sets the entire z index to the current z position and resets the previous timepoint to 0.
 +Simply save the code as a text file in the >​Macros>​Toolsets folder. It will show up in the toolsets dropdown under the name of the text file, Hyper with Stacks or whatever you name it.
 +Using FIJI on a Mac this folder is found by selecting show package contents on the FIJI application.
 +<code java>
 +// Hyper with Stacks.txt --version--1.5 ​ 2011-09-23
 +// Initial Toolset for manually extracting focused time series from hyperstacks by William J. Ashby, Vanderbilt University, Chemical and Physical Biology
 +// "​Summary of your worthwhile addition"​ by "Your Name" and "Your Institute ..."
 +var v=versionCheck();​
 +function versionCheck() {
 +    requires("​1.41f"​);​
 +    return 1;
 +var stackOrder = newArray("​xyzct",​ "​xyczt(default)",​ "​xyctz",​ "​xyztc",​ "​xytcz","​xytzc"​);​
 +var displayMode = newArray("​Color",​ "​Composite",​ "​Grayscale"​);​
 +var zNum=0; var cNum=0; var tNum=0; var zz=0; var cc=0; var tt=0;
 +var zArray; var width; ​ var height;
 +var initialize = true;
 +var t0=0;
 +macro "Blank Action Tool - "{
 +macro "Stack to Hyperstack Action Tool - C000D00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D11D12D13D15D16D1bD1cD1dD1eD1fD20D21D22D23D2bD2cD2dD2eD2fD30D31D32D33D34D38D39D3aD3bD3dD3eD3fD40D41D42D43D44D48D49D4aD4dD4eD4fD50D51D52D53D54D57D58D59D5aD5dD5eD5fD60D61D62D63D64D67D68D69D6aD6dD6eD6fD77D78D79D85D86D87D88D89D8aD8bD96D97D98D99D9aDa7Da8Da9Db0Db8CfffD14D17D18D19D1aD24D2aD3cD47D70D71D80D81D82D8fD90Da0Da1Da2Da3Da4DadDaeDafDb1Db2Db3Db4Db5DbcDbdDbeDbfDc0DccDcdDd0DdaDdcDddDe0De8De9DeaDecDedDf0Df8Df9DfaDfcDfdCf00D91D92D93Dc1Dc2Dc3Dc4Dc5Dc6Dd1Dd2Dd3Dd4Dd5Dd6Dd7De1De2De3De4De5De6De7Df1Df2Df3Df4Df5Df6Df7C00fD29D8cD9eD9fDcbDceDcfDdbDdeDdfDebDeeDefDfbDfeDffC0f0D25D26D27D28D35D36D37D45D46D4bD4cD55D56D5bD5cD65D66D6bD6cD72D73D74D75D76D7aD7bD7cD7dD7eD7fD83D84D8dD8eD94D95D9bD9cD9dDa5Da6DaaDabDacDb6Db7Db9DbaDbbDc7Dc8Dc9DcaDd8Dd9"​{
 +// In order to make my personal defaults automatically appear in the "Stack to Hyperstack‚Ķ"​ command, the following lines of code recreate the dialog window, display my recreation and allow user modification as necessary, and then run the "Stack to Hyperstack‚Ķ"​ with the values provided from the dialog window.
 +//  Customize the defaults below when working with multiple files of data that have identical numbers of channels, z-slices, and timepoints
 + Dialog.create("​Convert to Hyperstack"​);​
 +     ​ Dialog.addChoice("​Order",​ stackOrder); ​ //the stackorder is found a few lines above and can be rearranged in order to put your default order first
 + // To make this macro use your default number of channels, slices, and time frames
 + // simply change the numbers 2, 5, and 1 in the following 3 lines of code.
 + Dialog.addNumber("​Channels (c):", 2);  ​
 + Dialog.addNumber("​Slices (z):", 5);  ​
 + Dialog.addNumber("​Frames (t):", 1);
 + Dialog.addChoice("​Display Mode:",​ displayMode); ​
 +   ​;​ //Displays the dialog box in order to get user input for the conversion from stack to hyperstack ​
 + //or hyperstack to hyperstack if you already have the data in a hyperstack ​
 + //​Assigning the entered values to variables ​  
 + ​ ans1=Dialog.getChoice();​
 + cNum=Dialog.getNumber(); ​
 + zNum=Dialog.getNumber(); ​
 + tNum=Dialog.getNumber(); ​
 + ans2=Dialog.getChoice();​
 + zArray = newArray(tNum);​ //​Initializing zArray which stores the index of in-focus z values over time
 + run("​8-bit"​); ​ //This line could possibly be omitted after testing for compatibility with other size stacks
 + run("​Stack to Hyperstack...",​ "​order="​+ans1+"​ channels="​+cNum+"​ slices="​+zNum+"​ frames="​+tNum+"​ display="​+ans2+""​);​
 +//End of dialog section
 + initialize=true;​
 + print("​\nInitialized"​);​
 +macro "F1 Set Focus Action Tool - C000C111C222D34D35D36D37D38D39D3aD3bD3cD44D48D54D58D64D68D74Da4Da5Da6Da7Da8Da9DaaDabDacC222C333C444C555C666C777C888C999CaaaCbbbCcccCdddCeeeCfffD00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD1fD20D21D22D23D24D25D26D27D28D29D2aD2bD2cD2dD2eD2fD30D31D32D33D3dD3eD3fD40D41D42D43D45D46D47D49D4aD4bD4cD4dD4eD4fD50D51D52D53D55D56D57D59D5aD5bD5cD5dD5eD5fD60D61D62D63D65D66D67D69D6aD6bD6cD6dD6eD6fD70D71D72D73D75D76D77D78D79D7aD7bD7cD7dD7eD7fD80D81D82D83D84D85D86D87D88D89D8aD8bD8cD8dD8eD8fD90D91D92D93D94D95D96D97D98D99D9aD9bD9cD9dD9eD9fDa0Da1Da2Da3DadDaeDafDb0Db1Db2Db3Db4Db5Db6Db7Db8Db9DbaDbbDbcDbdDbeDbfDc0Dc1Dc2Dc3Dc4Dc5Dc6Dc7Dc8Dc9DcaDcbDccDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDdfDe0De1De2De3De4De5De6De7De8De9DeaDebDecDedDeeDefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDff"​{
 + run("​Set Focus [F1]"​);​
 +macro "Set Focus [F1]" {
 + Stack.getPosition(cc,​zz,​tt);​
 + if(initialize){
 + initialize=false;​
 + if (zArray==0){
 + if (Stack.isHyperstack) {
 + Stack.getDimensions(width,​ height, cNum, zNum, tNum);
 + zArray=newArray(tNum);​
 + print("​\nInitialized"​);​
 + } else {
 + print("​Close the error window and click the Run Stack to Hyperstack button"​);​
 + }
 + }
 + Array.fill(zArray,​ zz);
 + t0=0;
 + }
 + for (i=t0; i<tt; i++){
 + zArray[i]=zz;​
 + }
 + if (t0<​tt) ​
 + print("​z is set to: "​+zz+" ​ for t: "​+t0+"​ through "+tt);
 + if (t0>​=tt) ​
 + print("​current t="​+tt+" ​ Proceed to t>"​+t0+"​ or re-initialize"​);​
 + else 
 + t0=tt;
 +macro "Split Stack Action Tool - R9077C888R9977R0977"​{
 +    if (nSlices==1)
 +      exit("​Stack required"​);​
 +    setBatchMode(true);​
 +    stack1 = getImageID;
 +    w = getWidth; h = getHeight; ​ title = getTitle;
 +    stack2 = 0;
 +    n = zArray.length+1;​
 +    Stack.getPosition(c,​z,​t);​
 +    for (i=1; i<n; i++) {
 +        showProgress(i,​ n);
 +        selectImage(stack1);​
 +        Stack.setPosition(c,​zArray[i-1],​i);​
 +        run("​Copy"​);​
 +        if (stack2==0) {
 +            newImage("​Focused_C"​+c+"​_"​+title,​ "​8-bit",​ w, h, 1);
 +            stack2 = getImageID;
 +        } else {
 +            selectImage(stack2);​
 +            run("​Add Slice"​);​
 +        }
 +        run("​Paste"​);​
 +    }
 +    setSlice(1);​
 +    setBatchMode(false);​
 +    print("​Successfully split out channel "​+c+"​\nTo split out a different channel using this z-index, \nsimply change the channel in the hyperstack and repeat"​); ​
 +macro "F2 ReInitialize Action Tool - C000C111C222D14D15D16D17D18D19D1aD1bD1cD24D28D34D38D44D48D54D85D86D8bD8cD94D9aD9cDa4Da9DacDb4Db8DbcDc5Dc6Dc7DccC222C333C444C555C666C777C888C999CaaaCbbbCcccCdddCeeeCfffD00D01D02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eD0fD10D11D12D13D1dD1eD1fD20D21D22D23D25D26D27D29D2aD2bD2cD2dD2eD2fD30D31D32D33D35D36D37D39D3aD3bD3cD3dD3eD3fD40D41D42D43D45D46D47D49D4aD4bD4cD4dD4eD4fD50D51D52D53D55D56D57D58D59D5aD5bD5cD5dD5eD5fD60D61D62D63D64D65D66D67D68D69D6aD6bD6cD6dD6eD6fD70D71D72D73D74D75D76D77D78D79D7aD7bD7cD7dD7eD7fD80D81D82D83D84D87D88D89D8aD8dD8eD8fD90D91D92D93D95D96D97D98D99D9bD9dD9eD9fDa0Da1Da2Da3Da5Da6Da7Da8DaaDabDadDaeDafDb0Db1Db2Db3Db5Db6Db7Db9DbaDbbDbdDbeDbfDc0Dc1Dc2Dc3Dc4Dc8Dc9DcaDcbDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDdfDe0De1De2De3De4De5De6De7De8De9DeaDebDecDedDeeDefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfbDfcDfdDfeDff"​{
 + run("​Re-Initialize [F2]"​);​
 +macro "​Re-Initialize [F2]" {
 +    initialize=true;​
 + print("​Re-initialized,​ proceed with selection of focused z slices"​);​
 +var pmCmds = newMenu("​Popup Menu",
 +        newArray("​Set Focus [F1]", "​Re-Initialize [F2]","​-","​Copy",​ "​Paste","​Rename..."​)
 + );
 +macro "Popup Menu" {
 +    cmd = getArgument;​
 +    run(cmd);
 +The above code is made freely available for use and modification in keeping with the Creative Commons license see [[http://​​licenses/​by-nc-sa/​3.0/​|CC Attribution-Noncommercial-Share Alike]]. ​ ImageJ/FIJI programmers and aspiring programmers are welcome to contribute here.  I, William J Ashby, the initial creator and first author invite others who make worthwhile contributions to add themselves to the list of authors both on this wikipage and in the above code.
 +=====Known Bugs=====
 +The program will throw an error if you start setting focus points (i.e. indexing z positions) on a stack without converting it to a hyperstack. ​ A message to run Stacks to Hyperstacks is displayed and the error doesn'​t cause problems otherwise in the program.
 +=====Future Additions/​Improvements=====
 +Anyone and everyone are welcome to take what I have started and implement new buttons and features. ​ You may also request additions to the toolset here but I will probably have to leave the development of future additions to others.
 +  - The ability to write the index of in-focus z positions to file and read in the index from this file.
plugin/stacks/toolset_for_manual_extraction_of_best-focused_z-slices_from_hyperstack/start.txt · Last modified: 2019/04/12 13:13 (external edit)