Region Image
Region image window
When you open any experiment by default first region will be opened. Segmentation overlay will be selected by default.
When you open any experiment by default first region will be opened. Scale bar overlay will be selected by default.

Move region image to window/tab

This feature is available in 1.4.
Starting with version 1.4, you can move region images to a window or tab.
Region image in tab
When a region image is placed on a tab, you can find region features in the "Regions" menu.
'Regions' menu

Open new region

Open new region
In order to open another region you should click on 'Open region' item in 'File' menu.
Selecting new region #
You can export region image by clicking on the 'Export as PNG' menu item in the 'Regions' menu. Then you need to specify the location of the file. When the export is finished, you will see a message notification. If extended depth of field (EDF) was used to process data the best focus place is not applicable and will not be available for selection.
When any region image is opened by default it shows best focus z-plane for each tile.
You can disable 'best focus' mode by clicking on the corresponding menu item in the 'Image' menu.

Switching z-plane

z-plane slider
When 'best focus' mode is disabled, by default it shows middle z-plane. You can switch z-plane of each region image by adjusting slider at the bottom. When you switch z-plane, corresponding images with selected marker channel will be loaded. Also segmentation mask of new z-plane will be loaded if Segmentation overlay is selected in Overlay manager.

FIJI tools

FIJI tools
In addition to main frame and region image frames you are able to interact with FIJI tools frame.
Zoom in/out tool
Here you can pick a 'lens' tool for zoom in/zoom out region image by clicking on left/right mouse button.
FIJI selection tools
Also you can switch between different selection tools such as Rectangle, Polygon, Oval etc. Once you picked any selection tool your choice will be saved and you can draw selection on any region image.
Draw selection on region image

Creating a population

When you draw any selection on region image you can right click on it and choose 'Add population' option in order to create population with selected cells (This doesn't work when you open experiment without segmentation).

Remove area

When you draw any selection on region image you can right click on it and choose 'Remove area' option in order to remove this area and cells within in it from the experiment. (This doesn't work when you open experiment without segmentation).
You can always revert removed area. Right click on removed area and choose 'Revert area' option.
When you draw any selection on region image you right click on it and choose ‘Export area’ option in order to save the selection as an image.
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Outline
Remove area