Blog

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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Screening a million compounds for the price of a few thousand?

Anne Carpenter

Biologists are coming up with more and more complex physiologically-relevant assay systems and scaling them up for screens. From co-cultured cells to C. elegans to 3D organoids and tumor spheroids, these assay systems can be challenging, expensive, lower-throughput, and/or rely on materials such as human primary cells that are in short supply.

Might there be a shortcut allowing you to screen a huge chemical library without the expense? If you have image-based screens of a large compound set on hand, this ...

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Help! Why do my output images seem all black?

Beth Cimini

Double clicking on the output images produced by CellProfiler sometimes opens up a screen in your operating system’s default image viewer that looks all black. This can make it seem like your pipeline didn’t work or didn’t produce the right output. However, this can happen for a couple of reasons:

(a) If you’re exporting objects and have only a few objects in your image
(b) If you’re exporting 16-bit images

This has to do with the fact that most non-scientific photo software is designed to show 256 levels...

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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 surroundings? Such experiments are often conducted using highly confluent cell cultures, tissue sections, or densely cell-packed organoids. At this level, clusters of cells gather, tightly bind and overlap to form cell niches, and often in a single area...

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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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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 confusing what each one does, and it’s not always obvious which ones you need for your experiment.

If you have mistakes in any of these modules, you may run across the dreaded errors ‘The pipeline did not identify any...

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Making it easier to run image analysis in the cloud: announcing Distributed-CellProfiler

Beth Cimini

There’s nothing more exciting than getting back a big batch of data from your automated microscope – finally, you have the results of your screen, your timelapse, or whatever you’ve spent the last weeks or months preparing.  That excitement can turn to sadness quickly though when you realize that neither your laptop nor the old general-use computer in the lab are up to analyzing thousands (or tens of thousands, or hundreds of thousands!) of images.  But, congratulations! You’ve reached an elite level of CellProfiler...

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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 other object you’ve designated (like segmenting nuclei from your DAPI channel).
  • Secondary objects are created around a primary object, and so they usually need two pieces of information – a primary...
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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 in mind phenotypes to measure, so you use CellProfiler to accurately The
...

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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 community; here at the blog we proactively post content that we think will be new and interesting to you. We encourage you to comment and start discussions on our posts – the blog is integrated with our forum so that the conversation...

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