The different acquisition fields are listed. You will also be able to launch the processing sequences and run the measurements. You can select fields by using classical list selection with left button, Ctrl and Shift. The fields images are imported in the Experiment tab.

Selection

Select All

Selects all the fields of the list.

Select None

Clears the selection.

Delete Fields

Deletes the selected fields (channel images, cells, and all data associated).

Delete Input Images

Deletes the files associated to the selected fields.

Delete Slices

Opens a dialog box to choose start and stop slices. If "OK" is pressed, it will delete all slices strictly before and stricly after the chosen slice, on the first selected Field.

View

Overlay

Opens channel images of the first selected field, as an image5D (overlay image).
Colors are defined in the settings of the structure (see Experiment).

Input Images

Opens channel images of the first selected field, as separate images.

Cells

Displays the cells of the current selected fields and opens the cell list.

Process

Process Nuclei

Check this box to run the nucleus processing chain on all selected fields. The segmented cells will be stored in the database.

Test

Runs the processing chain on the first selected field 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.

Crop Cells

Check this box to crop all channel files according to the bounding box of segmented cells.

Process Structures

Check this box to run the processing chain to segment the different structures in all selected fields.

Quantifications

Check this box to perform quantification on cells of selected fields.

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 cells of the selected fields are overwritten.

Run

Runs the selected actions on selected fields.

Manual Segmentation

You can manually improve the results of the segmentation by deleting uncorrect segmentation, add cells not detected, and adjust the segmentation of some cells (like merging of close cells).
clicking will show the manual segmentation interface. This might take a few seconds because it retrieves the segmented cells of the current field.
See the manual nucleus segmentation page for details.

Export Quantifications

Export quantifications to spread-sheet compatible format and opens ImageJ Results Tables.
One file is generated per structure (with quantifications on objects), plus one file per couple of structure (with quantification between two objects).