Exchanging Images between ZEN core and 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:
- The ImageJ tool is selected.
- An image is displayed.
- Send the image to ImageJ by clicking the Send Image button.
- The image is sent to ImageJ. Any modifications (e.g. processing or measurements) are applied before it is sent.
- Follow the instructions in ImageJ.
- 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:
- The ImageJ tool is selected.
- Open ImageJ and prepare the image you wish to retrieve.
- 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. |
|
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. |
|
MD image |
All channels or layers are imported into a corresponding multidimensional image. |
|
Tiled image |
Partially supported |
Only the first tile is imported. |