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 EVIDENT(Olympus) vsi/oir/omp2info file formats and show some meta data.

New release

Ver.2.4.1 Fix for incorrect colours displayed in some VSI files.

Download

Download the latest OlympusViewer ImageJ Plugin for Windows and Mac.

Installation

Please see our installation instructions for Windows and Mac.

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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