Beth Cimini

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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Announcing CellProfiler 3.1.9

Beth Cimini

Hello all! It’s been a crazy last few months for the CellProfiler team, as we’ve been hiring some new members to the team and working hard on the transition to Python 3, which will bump us into CellProfiler version 4. Keep your eyes peeled for exciting content in the future!

We did want to bring you one last release in the 3.X series, though, especially for OSX 10.14 users who have been left without a useable build. This release also has some minor bugfixes in RelateObjects and IdentifySecondaryObjects.

As...

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Announcing CellProfiler 3.1.8

Beth Cimini

Happy holidays to everyone- we here at the CellProfiler team got you a little end-of-year treat in the form of CellProfiler 3.1.8.  This is primarily a bugfix release, getting rid of some bugs in MeasureObjectIntensity, MeasureColocalization, ExportToSpreadsheet, CorrectIlluminationCalculate, and Smooth.  We’ve also updated how we package for Windows, so those of you who had JAVA_HOME issues with 3.1.5 (feel free to now unset that in your environment variables if it’s set to your 3.1.5 install!) should now experience...

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Announcing CellProfiler 3.1

Beth Cimini

I’m excited to announce the release of CellProfiler 3.1.

Our focus for CellProfiler 3.1 was polishing features and squashing bugs introduced in CellProfiler 3.0. We also started laying down the foundation for our next release, CellProfiler 4.0, that will transition CellProfiler from Python 2 to Python 3, improve multiprocessing, and overhaul the interface.

There’re a few noteworthy changes that some users might enjoy like UTF-8 pipeline encoding, a simpler application bundle (that won’t require installing...

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The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part I: Using the new Test Mode

Beth Cimini

Everyone here at the CellProfiler team is very excited about our new 3.0 release, and we certainly hope you are too!  CellProfiler 3.0 is much faster than any of our previous releases, and the addition of volumetric processing is a huge game changer.

CellProfiler 3.0 looks pretty similar to what you’re used to, albeit a bit sleeker than previous versions. While most of it still behaves exactly how you’re used...

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The CellProfiler 2 User’s Guide to CellProfiler 3.0, Part II: Converting your pipelines

Beth Cimini

For those of you who’ve been with us for a long time though, the obvious next question after how to use the new test mode is will my old CellProfiler pipelines work in the new version? We feel the same way – the pipelines you’ve accumulated over the years are precious resources!  The good and bad news is that the answer is Yes, mostly. In order to facilitate the...

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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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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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