A explained previously on the Project page, a project is a raw (one-level) list of images without any link between these images:
In some studies, one might want to link images because they are somehow related, e.g. all images of a sample acquired following different preparation (e.g. IHC staining) or acquisition protocols (e.g. different scanners/microscopes).
The ImageGroup concept is a a list of images that are related. This concept therefore allows to link multiple, multimodal images. Thanks to the concept of image groups, annotation can also be linked between images e.g. to link a region of interest in Image A to other regions of interest in Images B, C, etc.
# Create an ImageGroup
To create an image group, go to the “Image groups” panel and click on ”Add image group”. First, choose a name for your new Image Group:
You will then be able to select images from your project and associate them to this image group:
You then have a list of image groups in your project (here 4 different image groups with different numbers of images in each). Here the last ImageGroup contains 10 images:
# Create Annotation Links
The concept of AnnotationLinks allows to link annotations in multiple images of an ImageGroup, e.g. to link different annotations corresponding to a common region of interest in a tissue (e.g. a specific tumor region in stained images or in images acquired with different equipments).
# Copy, paste, and link an existing annotation to other images of the Image Group
To create an annotation and paste-link it in other images, first draw a precise annotation (in the reference image) as usually using annotation tools in a single viewer (see Annotation page ). If you want to associate an ontology term to it (e.g. Tumor), use the Ontology tool. Here we illustrate a use-case where annotations have already been created in 5 images, and the user wants to paste an annotation to a sixth image:
Then, open the whole image group in a multiviewer. Select and copy the annotation in the original image using the Copy Icon (top toolbar).
If images are not aligned, you should move the different viewers into the approximate right position (and eventually rotate images using rotation tool).
Click on “Paste with link” icon (top toolbar)
Select images from the imagegroup where you want to paste the annotation. In this example, we will only paste the annotation in the sixth image:
If images are perfectly aligned you can use “original annotation position” that will paste the annotation at the exact same (x,y) location in the target images. If images are not aligned choose “viewer center position” (this will paste the annotation at the center position of each viewer). This will create annotation links and copy annotation geometry+term in all images in one single operation.
If images are not perfectly registered, pasted annotations are not at the exact right position and size and could be edited.
# Create two distinct annotations and link them
If editing a pasted annotation is too complex (e.g. if it requires more clicks to correct it than drawing the annotation from scratch) or if linked annotations are too different (e.g. because images were aquired with very different spatial image resolution and therefore the mapping between the modalities is not direct as images are dissimilar), it is possible to create distinct annotations in distinct images and link them afterwards. To do so, using the multiple image viewer, you can make a new annotation from scratch, then link it to another (reference) annotation. To do so, select the reference annotation in the viewer of the corresponding image, select your new annotation in the right viewer, and use the link button (top toolbar): confirm link by selecting the annotation (should be highlighted in blue).
Note that if you have an Annotation A and you link it to an annotation B (previously linked to C,D), then annotation A will also be linked to C,D, so you can select any annotation from the annotation group and it will add your annotation to it. If you want to unlink an annotation, use the unlink icon:
# View and navigate through Groups of images and annotations
Once images are grouped or annotations are linked, it is possible to navigate through them, and combine it with the multi-image viewer to compare images and annotations, etc.
Once you click on an annotation, the current selection dialog box now displays its linked annotations, and by clicking on them you can open the linked annotation in the corresponding image of the Imagegroup. You can also open the annotation in another panel of the multiple image viewer, or click on "Show all linked annotations" to split the screen and view all the linked annotations at the same time. It is also possible to select an annotation and use keyboard shorcuts (Ctrl + -> or Ctrl + <-) to go to the next (previous) annotation in this group. You can go back and forth.
When using the multiple image viewer, you can also browse from one image to another in this ImageGroup using "Previous image in group" or "Next image in group":
Linked annotations can also be seen in the Annotations Tab of the project and filtered by Image group (a black line surround linked annotations):