napari-imagegrains Processing Image Segmentation#
This widget allows you to perform image segmentation on your data. You can open it via Plugins -> ImageGrains -> ImageGrain Processing Widget.
Define folder locations#
When using the demo data provided, you start with a default situation. A model folder with two models is provided as well as an image folder with two images. Models and images are displayed in corresponding lists and can be selected upon mouse click. When selecting an image, it appears in the viewer. Under custom conditions, you start by indicating with Select model folder and Select image folder where your models and images are located. After that, you can select individual models and images to work with.
Explore image segmentation#
You can explore the image segmentation by chosing Run segmentation on selected image. The segmentation prediction (mask) will be displayed in the viewer on top of the selected image. Under Segmentation options you can check the Save prediction(s) checkbox in order to save the segmentation mask in the path you provide in Save prediction(s) to.
Be aware that a very large image requires some time to be segmented.
Manually process segmentation mask#
You can manually process the segmentation prediction by setting the label on the left side of the viewer to 0 and performing drawings. By clicking on Save manually processed mask you can save the processed mask in the path below.
Segmentation options#
Load initial prediction#
If you want to reload the initial prediction, check Load prediction(s), select another image from the image list and then select the initial image again. The initial prediction mask is reloaded.
