OlympusImageJPlugin


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

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

Installation

Please see also installation manual.

Windows

Download OlympusViewer-win.zip here
Extract the zip file.
Execute OlympusViewer-win.exe. This file is in self-extracting format.
If you agree to our end user license agreement, extract it to your specified folder.
Unzip the OlympusViewer-package.zip
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
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

Download OlympusViewer-mac.dmg here
Double click the dmg file.
If you agree to our end user license agreement, extract it.
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

Select a menu item Plugins › OlympusViewer › Viewer
Select a file.

Show Meta Data

Select a menu item Plugins › OlympusViewer › ShowInfo

Drag & Drop (ver2.1.1-)

Select a menu item Plugins › OlympusViewer › DragDrop
Drop a image file.

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

Select a menu item Plugins › OlympusViewer › DragDrop › Use Virtual Stack for large images
Drop a image file.

Use Macro function (ver2.3.1-)

Enable Macro Record function.
Select menu item Plugins › OlympusViewer › Viewer
Select image file.
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

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