Preprocessing¶
This section describes the data processing functionalities available in
PlantSeg Interactive. This functionalities are available in the
Preprocessing
tab in the PlantSeg Interactive GUI.
Widget: Crop¶
To crop an image, first add a Shapes
layer. You find the Add Shapes Layer
button above the layer list on the left side. With the Shapes
layer selected,
you can add one rectangle using by pressing R
and drawing.
In the Crop widget, you can also crop on the z dimension if applicable.
- Crop shapes layer: This must be a shape layer with a rectangle overlaying the area to crop.
- Z slices [start, end): Number of z slices to take next to the current selection. START is included, END is not.
Widget: Image Rescaling¶
Many boundary prediction models are sensitive to the scale of the input.
Use the To model voxel size
option to match your input to your desired model.
Using the From factor
mode, the user can rescale the image by a multiplicate factor.
For example, if the image has a shape (10, 10, 10)
and the user wants to rescale it by a factor of (2, 2, 2)
, the new size will be (20, 20, 20)
.
Rescale an image or label layer.
Using the To layer voxel size
mode, the user can rescale the image to the voxel size of a specific layer.
For example, if two images are loaded in the viewer, one with a voxel size of (0.1, 0.1, 0.1)um
and the other with a voxel size of (0.1, 0.05, 0.05)um
, the user can rescale the first image to the voxel size of the second image.
Rescale an image or label layer.
Using the To layer shape
mode, the user can rescale the image to the shape of a specific layer. For example, if two images are loaded in the viewer, one with a shape (10, 10, 10)
and the other with a shape (20, 20, 20)
, the user can rescale the first image to the shape of the second image.
Rescale an image or label layer.
Using the To model voxel size
mode, the user can rescale the image to the voxel size of the model.
For example, if the model has been trained with data at voxel size of (0.1, 0.1, 0.1)um
, the user can rescale the image to this voxel size.
Rescale an image or label layer.
Using the To voxel size
mode, the user can rescale the image to a specific voxel size.
Rescale an image or label layer.
Using the To shape
mode, the user can rescale the image to a specific shape.
Rescale an image or label layer.
Using the Set voxel size
mode, the user can set the voxel size of the image to a specific value. This only changes the metadata of the image and does not rescale the image.
Rescale an image or label layer.
Widget: Gaussian Smoothing¶
Apply Gaussian smoothing to an image layer.
- Sigma: Define the size of the gaussian smoothing kernel. The larger the more blurred will be the output image.
Widget: Image Pair Operations¶
Apply an operation to two image layers.
- Layer 1: First image to apply the operation.
- Layer 2: Second image to apply the operation.
- Operation: None
- Normalize input: Normalize the input images to the range [0, 1].
- Clip output: Clip the output to the range [0, 1].
- Normalize output: Normalize the output image to the range [0, 1].