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OlympusImageJPlugin
Formats | |
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Bio-Formats | |
Video formats | |
QuickTime | |
TIFF | |
DICOM | |
Zeiss LSM | |
Olympus VSI | |
Opera Flex | |
All I/O plugins |
OlympusViewer Plugin (ImageJ) | |
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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. |
Initial release | Dec. 9, 2015: First version Ver.1.1.1 |
Latest version | Mar. 17, 2020: Ver.2.3.1 |
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
- 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
See Also
This plugin uses jai-imageio.