It is plane to Z how FIJI is a great companion for visually verifying CellProfiler’s 3D segmentation

Now that CellProfiler can handle 3D images, how do you view the results? When processing 2D images, the IdentifyPrimaryObjects module will produce a figure that displays the original image next to the segmented image to make validation fast and convenient, a side-by-side comparison. However, the extra dimension in 3D complicates this approach, because the 3D image must be transformed in some manner in order to appear on a flat surface (e.g. the monitor or phone you’re using to read this blog post!). This blog post contains advice on how to look at 3D images and the 3D segmentation image produced by CellProfiler and introduces orthoviews in FIJI. If you would like to explore the example used in this post please check out the demo posted on the CellProfiler forum. Continue reading

CellProfiler & Ilastik: Superpowered Segmentation

Joining forces

CellProfiler is capable of accurate and reliable segmentation of cells by utilizing a broad collection of classical image processing methods. Peruse the documentation on the IdentifyPrimaryObjects module, for example, to get a sense of these, e.g., thresholding, declumping, and watershed. However, despite the many problems CellProfiler can readily solve, certain types of images are particularly challenging. For instance, when the biologically relevant objects are defined more by texture and context than raw intensity many classical image processing techiques can be foiled; DIC images of cells are a common biological example.

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