The detected cells are listed on the list with names and associated thumbnail. You can delete unwanted cells, view them in Image5D by clicking View cells (original and segmented images will appear). You can open the different channels by clicking Open Structures. A 3D view is available using the 3D viewer plugin by clicking 3D. A tag can be associated with each cell, for instance the degree of confidence on the segmentation or the quality of the image by using the tag list (-1 for bad, 0 for unknown, and a quality index ranging from 1 to 10).

Selection

Select All

Selects all the cells on the list.

Select None

Clears the current selection.

Delete Cells

Delete selected cells. All associated images and data will be lost.

Tags

Tags are useful to mark certain categories of cells manually.
Cells are displayed with the associated color in the list.
Tags are retrieved along with quantifications.
When cells are marked with the tag "-1" they are ignored.

View

Overlay

Displays an overlay view of the raw and segmented images of the first selected cell of the list using Image5D. Colors of structures can be edited in the Experiment tab.

Open Structures

Open the raw and segmented image of the selected structure of the current cell.

View 3D

Displays a 3D representation of segmented cell and associated objects.
Settings of each structure can be edited in the Experiment tab.

Objects

Show the Objects manager to browse the objects of the selected structure of the current cell.

Process

Process Structures

Check this box to run the processing chain on selected cells.

Quantifications

Check this box to perform quantification on all selected cells.

Override Quantifications

When performing quantification, if this box is unchecked, only quantifications that haven't been performed yet will be done. Otherwise, all quantifications of the selected cells are overwritten.

Test

• If process structure is checked, runs the processing chain on the first selected structure of the current cell, in "verbose" mode. The resulting segmented image is not stored in the database.

The verbose mode allows to show intermediate images, messages in log (like threshold values...), to help tuning the processing chain.

• If quantification is checked, it will perform quantifications on the selected cell, in "verbose" mode, without storing them.

Run

Runs the selected actions on selected structures of selected cells.