This grid will later be used to interpolate feature values over, so that we can assign a value to each point in the point cloud. Once the stack has been created, a 2D grid will be created that covers the aligned tissue sections with its width determined by the nx parameter. It is assumed that the tissue sections have been stained with Hematoxylin and Eosin.Uneven section thickness and staining can also affect the segmentation performance. This could for example be classifications, hair, folds, bubbles or dust. The cell segmentation is based on color intensity and might therefore fail if artifacts are present in the HE images.The Create3DStack() will automatically reload the images in higher resolution if the image widths are lower than 400 pixels or you can run SwitchResolution() to reload the images in higher resolution before running Create3DStack() The images have to be loaded in higher resolution than the default 400 pixels.HE image has to be aligned, i.e. you have to run LoadImages(), MaskImages() and AlignImages() (or ManualAlignImages()) first.The sections have to come from the same tissue type with similar morphology for each section.Below are a couple of criteria that has to be fulfilled for the method to work: Feature values can be interpolated across the points in the stack and then visualized in 3D by mapping the values to a colorscale. Once the nuclei coordinates have been extracted from each aligned section, a z value will be assigned to each section to create a 3D stack. This is not an exact cell segmentation but it will typically capture the density of nuclei well enough to define various morphological structures. The cell nuclei coordinates are extracted based on color intensity as nuclei are typically darker in color than the surrounding tissue.
STutility currently allows for visualization of features in 3D using a point cloud created from the nuclei detected in aligned HE images using the Create3DStack() function. Wflow_publish(files = c("analysis/index.Rmd", "analysis/about.Rmd", Updated website with new theme and content
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