Special Modules & Extensions

You activate the ImageJ extension via the Extensions Manager and then configure it in the Options dialog.

Configuring the Software

1. ImageJ is installed on your system.
   The Life-Line version of the Fiji distribution is recommended, which contains all necessary ImageJ plugins and works with .
2. You are logged in as an administrator.
3. The Home Screen is displayed.

1. Activate the ImageJ Extension in the Extensions Manager:
2. Maintenance > Extensions Manager
2. Confirm the configuration by clicking the Apply button.
3. If you activate ImageJ for the first time, a "missing path" warning is displayed. Confirm by clicking OK.
3. Open the Options window:
4. Maintenance > Options
4. Select the ImageJ tab.
5. Select the path to the ImageJ executable from the drop-down list:
6. Select one of the paths suggested by the software.
7. Click on to specify a different path.

Configuring ImageJ

To configure how ImageJ interacts with the software:

1. ImageJ is installed on your system.
   The Life-Line version of the Fiji distribution is recommended, which contains all necessary ImageJ plugins and works with the software.

1. Open the ImageJ installation specified in the software options.
2. Activate the Single Instance Listener:
3. You find the Single Instance Listener under Edit > Options > Misc…

The ImageJ extension of requires ImageJ to be installed and additionally to be configured correctly.

To prepare ImageJ for the use in , perform the following steps:

1. Create a folder which can be fully accessed without Windows administrator rights.
2. Install ImageJ in the created folder. Check for ImageJ updates after installation.
3. We recommend to use the Fiji distribution, which includes all required plugins. If you use Fiji, you can skip the next two steps.
3. Download the OME Bio-Formats library (LOCI Plugins for ImageJ).
4. Copy the downloaded file loci_tools.jar to the ImageJ\plugins folder.
5. Make sure that Run single instance listener is activated in ImageJ.
6. You find it under the Edit > Options > Misc…

ImageJ is now correctly installed and prepared to work with the software. If you have several ImageJ installations on your computer, make sure to direct the software to the above installation using the General Options dialog.

The ImageJ workbench enables you to connect with ImageJ. The communication between the two programs is bidirectional. You can use ImageJ to complement the image processing tools available in .

1. ImageJ is installed on your system and configured for .
2. The ImageJ Extension is activated in the software and configured.
3. Your are logged in as a supervisor.

1. Add the ImageJ Connection workbench:
2. + Add Task > Utilities > ImageJ Connection > + Add
2. Use the Send Image and Retrieve Image buttons to send the image to ImageJ and to retrieve it back into the software after processing it with ImageJ.

The ImageJ tool enables you to send images to ImageJ or to retrieve images from ImageJ, e.g. after processing them with ImageJ.

Sending or Retrieving Images

Sending an image to ImageJ

To send an image to ImageJ:

1. The ImageJ tool is selected.
2. An image is displayed.

1. Send the image to ImageJ by clicking the Send Image button.
2. The image is sent to ImageJ. Any modifications (e.g. processing or measurements) are applied before it is sent.
2. Follow the instructions in ImageJ.
3. Depending on the image data, ImageJ shows an import dialog. For more information, see the ImageJ instruction manual.

Retrieving an image from ImageJ

To retrieve an image from ImageJ:

1. The ImageJ tool is selected.

1. Open ImageJ and prepare the image you wish to retrieve.
2. In , click the Retrieve Image button in the ImageJ tool.

Image Type Conventions

ImageJ does not support all file types and pixel types that can be used in the software.

In these cases the image must be converted in the software before sending it to ImageJ.

See the tables below for further details.

to ImageJ

	ImageJ	Comments
.tif, .jpg, .bmp, .png, .gif	Original	The image is imported unchanged.
.ome.tif	Original	The image is imported unchanged.
.czi 2D 8/16 Bit B/W	32 Bit RGB	You can change the pixel type back to B/W in ImageJ using the Image > Type command.
.czi 2D 12 Bit B/W	Not supported	Convert the image to 16 bit B/W using the Change Pixel Type tool before sending it to ImageJ.
.czi 24/48 Bit RGB	32 Bit RGB
.czi 36/42 Bit RGB	Not supported	Convert the image to 24/48 bit RGB using the Change Pixel Type tool before sending it to ImageJ.
Multi-channel Z stack Temperature/Time series	MD image	If necessary, reassign the dimensions in ImageJ using Image > Hyperstacks for example.
Tiled image	Partially supported	Only the first tile is imported.

ImageJ to

ImageJ		Comments
.tif, .jpg, .bmp, .png, .gif	Original	The image is imported unchanged.
.ome.tif	Original	The image is imported unchanged.
2D images, B/W or RGB	.tif, B/W or RGB	Any 2D image other then the types listed above is received as a .tif-image.
Multi-channel Z stack Temperature/Time series	MD image	All channels or layers are imported into a corresponding multidimensional image.
Tiled image	Partially supported	Only the first tile is imported.