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Region annotation workflow with SCiLS Lab and SCiLS Cloud

Regions of interest (ROI) can comfortably be created in SCiLS Cloud and imported into SCiLS Lab. In SCiLS Cloud only a reference image is needed for creating the ROIs. The ROIs can be downloaded and imported into SCiLS Lab where the reference image is used to match the region information to the imaging mass spectrometry data.

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Creating regions in SCiLS Cloud requires only a couple of steps:

  • Upload the reference image
  • Optionally share the reference image with an expert
  • Create the regions of interest
  • Download exchange file
  • Load exchange file into SCiLS Lab

In the following they are explained in further detail.

Step 1: Annotate regions in SCiLS Cloud.

To create regions in SCiLS Cloud, you first have to upload a reference image to your personal account using the upload tool. Accepted file types for uploading are .jpg, .tif, and .png. If you do not want to draw the regions yourself, because you might want to rely on the opinion of an expert, you can grant other users access to the reference image in SCiLS Cloud. The ROIs will automatically be synchronized between all users with access to the reference image.

Navigate to the list view of all datasets in SCiLS Cloud and click open on the title card of the reference image you want to create ROIs for. SCiLS Cloud will change to the Region Annotation view. Use the zoom and pan options to locate the starting point of your ROI.

Once you are ready, click the pencil button [] to start drawing the polygon. Each click with the mouse will add a vertex to the polygon. Clicking and dragging the mouse allows you to move the reference image. While you are in edit mode, use the mouse wheel to zoom in our out. You can undo your last click by hitting the backspace button on your keyboard. Close the polygon to finish the ROI by clicking the first vertex of the entire polygon. Next to the closing vertex, a naming box appears, where you can assign a custom name or use the default name.

Repeat drawing regions until you are finished. When you are finished, click the pencil button [] again to leave the drawing mode.

The annotation view of SCiLS Cloud. In the top left corner are the navigation controls, the top right corner shows the editing controls. Solid areas with name denote regions from active overlay, dashed areas show regions from non active overlays.

Manage and delete regions.

Regions can at all times be edited in SCiLS Cloud. Select the region you want to edit and click the wrench tool []. The individual vertices go into edit mode as does the name box. While in edit mode, you can change the position of any vertex by clicking and dragging the rectangle connected to the edges of the ROI. Also while in edit mode, the confirm [] and cancel [] buttons appear next to the name box. To confirm your changes click the check mark; to cancel the editing click the cross icon.

Selected regions can be deleted using the trash button []. Note that deleting regions cannot be undone.

Organizing regions into different overlays.

You can also organize your regions into distinct overlays. Overlays are created using the plus button [] next to the selection drop down menu. The new overlay is directly activated, while visible regions from inactive overlays are marked with a dashed line. To make inactive overlays invisible, click the eye icon () in the drop down list.

Note that the overlays need to be present before you start creating your ROIs; it is not possible to change the association of regions and overlays. It is only possible to rename overlays which is achieved by clicking the pen icon behind an overlay’s name.

If you want to delete one overlay, you can do so by clicking the cross button [] behind the name. Only the active overlay is deleted, but all ROIs associated with this overlay are deleted as well.

Step 2: Downloading region annotations into SCiLS Lab.

When you are satisfied with the newly created regions, use the download button [] to create all necessary information for SCiLS Lab. SCiLS Cloud will create an exchange file (.sef) that contains both the image and the regions of interest. Normally, your download will start directly. However, if the file is large, then SCiLS Cloud will offer to send you the download link via email.

In SCiLS Lab, go to File > Import > Region (SCiLS Exchange Format) and open the .sef file downloaded from SCiLS Cloud. If the reference image is already present in SCiLS Lab, then the ROIs are checked whether or not they contain any spectra. All importable regions are listed in the next screen. Here you can select into which existing region you want to import them. If necessary, the polygons will be reduced to the extent of the already existing regions.

If the reference image is not present, then you are asked to align the reference image you used in SCiLS Cloud to one of the existing images in SCiLS Lab. This is done by matching two reference points in the two images. For more details about this step, see the SCiLS Lab Manual, Section 4.5.4 Importing optical images (co-register new image) and Section 4.5.5 Transferring region annotations between files.

Step 3: Perform analysis in SCiLS Lab.

With the previous steps you managed that the region annotations are present in your SCiLS Lab file. Note that only those regions can be imported for which you have spectra available in your file. Regions that do not contain spectra will be removed and the region’s polygons might be reduced in such a manner that no blank areas will be created. Despite these restrictions, you can work with the regions from SCiLS Cloud as if they were created in SCiLS Lab and perform any analyses based on this information.

Overview of the navigation and editing controls.

In the top left corner of the drawing canvas, are the navigation controls. The top right corner contains the editing controls.

  • Zoom in/out
    Zoom in/out to the dataset, also works with the mouse wheel.
  • Reset zoom
    Reset the zoom to show the entire image.
  • Rotate left/right
    (This icon is only available if you can edit the dataset.)
  • Flip horizontally/vertically
    (This icon is only available if you can edit the dataset.)
  • Create/edit region
    Create or edit a region.
  • Delete region
    Delete the currently selected region.
  • Add overlay
    Add a new overlay for grouping regions.
  • Delete overlay
    Delete the active overlay and all containing regions.
  • Download file
    Download entire file for use in SCiLS Lab.
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