After you’ve finished drawing click on the “Labkit Pixel Classification” button under Segmentation and then click the “gear” icon to access the “Pixel Classification Settings” Window. Switch to the foreground label and draw on the image to train the classifier as to what you consider to be foreground.ħ. Then proceed to draw on your image to train the classifier what you consider to be background.Ħ.

The size of the pen “tip” is adjusted with the brush size slider and by default the background label is selected.

Once you’ve adjusted your channel(s) display and are ready to train the classifier switch to the pen tool in the top menu bar. However, segmentation results as label images from Labkit, ilastik, StarDist, and other open source tools can now be imported into Imaris as Surfaces via a new Import Button within the Surpass View.ĥ. The Labkit integration within Imaris permits the creation of 1 Surfaces component at a time.GPU-acceleration should be used when possible.Often it is best to draw small regions than to draw large regions for the classifier training due to the fact that Labkit uses every drawn pixel for training and that can consume a lot of computer resources without improving results much.Use the “Reset View” option under the View menu to revert to an XY view. Heavy users of Imaris may inadvertently rotate their image.Use the right mouse button to pan and the left mouse button to rotate.To zoom in Labkit hold Shift + Ctrl while using the scroll wheel.Within Labkit the scroll wheel allows you to scroll through the 2D planes of the image as it’s orientated.

As with BDV the mouse controls for zooming are different than in Imaris.

Click the Settings button in the upper left corner of Labkit to reveal a window panel for display adjustments for each channel.

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