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Be a Histology Hero with CellProfiler

Minh Doan Thanks to the rapid advancement in image processing, we now have so many techniques to characterize cellular and subcellular objects (hooray CellProfiler!) Measuring cultured cells in monolayers is (usually) easy…but what about examining how cells interact with each other and their...

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...

Help! Why does CellProfiler say it can’t find any valid image sets?

Beth Cimini Defining the input to CellProfiler can be the hardest part of getting your pipeline set up and your analysis underway. Incoming images are configured in the first 4 modules of CellProfiler – Images, Metadata, NamesAndTypes, and Groups – which offer lots of flexibility. But it’s sometimes...

Help! What are these three different modules to identify objects?

Beth Cimini It can be confusing when you’re trying to set up your first pipeline to figure out which modules to use to generate your objects! A helpful way to understand the difference between Identifying Primary, Secondary, and Tertiary objects: Primary objects are segmented independently from any...

Looking for the Unexpected: Unbiased Image Analysis

Anne Carpenter So you already know how to put together an image analysis pipeline to measure particular phenotypes of interest? Great! Have you ever considered looking for the unexpected? Say you are comparing two treatment conditions, such as a negative control vs. a hormone treatment. You may have...

Welcome to the CellProfiler Blog!

CellProfiler Team The CellProfiler team is excited to announce the launch of our new blog! Articles will have a variety of topics, ranging from general knowledge, to specific module use and relevant literature spotlights. At the CellProfiler Forum, we answer all kinds of questions straight from the...