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OlympusImageJPlugin

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    Name

    OlympusViewer Plugin

    Software

    ImageJ

    Author

    OLYMPUS CORPORATION (olympus-imagejplugin at ot.olympus.co.jp)

    Maintainer
    Source

    The source code of plugin is in Olympus_Viewer.jar. The source code of native library is not provided.

    Status
    Category

    :Category:Import-Export

    This plugin can load Olympus vsi/oir/omp2info file formats and show some meta data.

    Installation

    Please see also installation manual.

    Windows

    1. Download OlympusViewer-win.zip here
    2. Extract the zip file.
    3. Execute OlympusViewer-win.exe. This file is in self-extracting format.
    4. If you agree to our end user license agreement, extract it to your specified folder.
    5. Unzip the OlympusViewer-package.zip
    6. Install vs2017 runtime if the runtime is not installed in your PC. The runtime is in OlympusViewer-package/WinRuntime. If you use 32bit OS, install VC_redist.x86.exe. If you use 64bit OS, install VC_redist.x64.exe
    7. Copy “OlympusViewer” folder in “OlympusViewer-package” folder to the plugins folder of your ImageJ directory. If ImageJ plugin folder already has OlympusViewer folder, delete the folder before copying.

    Mac

    1. Download OlympusViewer-mac.dmg here
    2. Double click the dmg file.
    3. If you agree to our end user license agreement, extract it.
    4. Copy “OlympusViewer-Ver2.3.1” folder to the plugins folder of your ImageJ directory. If ImageJ plugin folder already has OlympusViewer folder, delete the folder before copying.

    How to use

    File Open

    1. Select a menu item ( Plugins -> OlympusViewer -> Viewer )
    2. Select a file.

    Show Meta Data

    1. Select a menu item ( Plugins -> OlympusViewer -> ShowInfo )

    Drag & Drop (ver2.1.1-)

    1. Select a menu item ( Plugins -> OlympusViewer -> DragDrop )
    2. Drop a image file.

    Virtual stack mode for large images (ver2.2.1-)

    1. Select a menu item ( Plugins -> OlympusViewer -> DragDrop -> Use Virtual Stack for large images )
    2. Drop a image file.

    Use Macro function (ver2.3.1-)

    1. Enable Macro Record function.
    2. Select menu item ( Plugins -> OlympusViewer -> Viewer )
    3. Select image file.
    4. You can see that Macro command was registered.

    Macro sample code

    Use GUI commands

    • Sample for opening an image:
    run("Viewer", "open=D:/image/test/test.oir");
    
    • Sample for opening an image which has multiple groups or levels:
    run("Viewer", "open=D:/image/test/test.vsi group1_level1");
    
    • Sample for opening images in a directory:
    input = "D:/image/test/";
    
    list = getFileList(input);
    for (i = 0; i < list.length; i++){
        path = input + list[i];
        run("Viewer", "open=[path]");
    }
    
    • Sample for batch processing:
    setBatchMode(true);
    
    input = "D:/image/test/";
    
    list = getFileList(input);
    for (i = 0; i < list.length; i++){
        path = input + list[i];
        run("Viewer", "open=[path]");
        // process image e.g. "run("Smooth", "stack");"
        saveAs("Tiff", "D:/image/test/out_" + i + ".tif");
    }
    

    Use programming interface

    You can use programming interface by using OVMacro command.

    • Sample for opening an image:
    run("OVMacro");
    Ext.openFile("D:/image/test/test.oir");
    
    • Sample for opening an image which has multiple groups or levels:
    run("OVMacro");
    Ext.openFile("D:/image/test/test.vsi", 1, 2); // Open Group 2, Level 3
    
    • Sample for opening images in a directory:
    run("OVMacro");
    Ext.openFolder("D:/image/test"); // You can specify group and level like as openFile
    
    • Sample for getting number of groups and levels:
    run("OVMacro");
    path = "D:/image/test/test.vsi";
    Ext.getGroupCount(path, groupNum); // Get total count of groups
    Ext.getLevelCount(path, groupNum-1, levelNum); // Get total count of levels
    Ext.openFile(path, groupNum-1, levelNum-1); // Open last level of the last group
    

    See Also

    This plugin uses jai-imageio.