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Labkit - Frequently Asked Questions

Is it possible to manually segment a 3D image slice by slice?

Yes, this can be achieved by a workaround: Simple convert your image to 2D+time before opening it with Labkit. In Fiji use “Image > Hyperstacks > Re-order Hyperstack …” to convert your image from 3D to 2D+time.

After starting Labkit the window that should show my image is black?

This often happens if Labkit can’t find proper brightness & contrast settings. Please click the button that says “auto contrast”.

How I manually select the colors and brightness settings that are used to show the image?

Click S on your keyboard. This should show the BigDataViewer brightness & color dialog. Use it to manually adjust those settings.

Can Labkit distinguish more than two classes “foreground” and “background”

Yes, simple click the “Add label” button this will add a new class. You are free to name labels / classes as you would like, simple double click on the label.

How can I change the color of the labels?

Just click on the colored rectangle left of the labels name. This will show a color selection dialog.