October 2019

When To Say ‘Good Enough’

Beth Cimini

One of the most common questions I’m asked when helping a collaborator with an image analysis project is:

“How do I know when my analysis workflow is doing well enough at finding the objects or measuring the things I care about?”

Unfortunately, it’s also one of the hardest questions to answer!  In an ideal world, we’d be able to achieve perfect recognition and/or segmentation of our biological objects every time, and get out perfect data! Alas, biology is almost never so...

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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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