Kyle Karhohs

A CellProfiler Approach to Analyzing Tissue Data

Kyle Karhohs

Imaging tissue slices provides a wealth of data about the spatial composition and number of the various cell types that make up a tissue. Interactions among cells within a tissue are crucial to understanding the role of the inflammation that is triggered by the invasion of cancerous cells. The strength of the inflammatory response has been linked to the prognosis of certain cancers such as lymphoma.

Quantifying the spatial relationship among cells in the crowded environment of a tissue requires reliable segmentation...

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Mo Data, Mo Problems: How to share big data with ease

Kyle Karhohs

# Sharing Image Data

At the Imaging Platform we frequently need to send and receive images between collaborators or forum users. Working with images can become challenging simply due to their file size. Memory and disk limitations are often irritants when analyzing images, but in some cases, such as multi-dimensional images and whole-slide scans, images’ file sizes can be large enough that even accessing images becomes a major roadblock, especially when the size starts to rival the size of desktop or laptop hard...

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

Kyle Karhohs

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...

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CellProfiler & Ilastik: Superpowered Segmentation

Kyle Karhohs

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...

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