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CellProfiler Analyst 3.0 Release: Accessible data exploration and machine learning for image analysis.

David R. Stirling

We have now released CellProfiler Analyst version 3.0! Download it here.

As with CellProfiler 4, the primary goal of this release has been to migrate from Python 2 to Python 3 and modernise the application. We’ve also focused on improving performance and usability. Along with backend improvements that make the software faster and more reliable (see...

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CellProfiler 4.0 Release: Improvements in speed, utility, and usability

David R. Stirling

We have now released CellProfiler version 4.0! Download it here.

The primary goal of this release has been to migrate CellProfiler from Python 2 to Python 3. This has involved extensive restructuring of the code base, leading to a lot of “under-the-hood” improvements.

Important Compatibility Notes

As a major release, this version contains changes to CellProfiler that will...

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Help! I want to use CellProfiler Analyst but I ran my pipeline with ExportToSpreadsheet!

David R. Stirling

We’ve all done this before – CellProfiler Analyst needs a database file, but your CellProfiler pipeline that took days to run was set up to export spreadsheets. To make matters worse, you also need a .properties file explaining what to do with that database. Fortunately, you don’t need to re-run the entire experiment to get your data into CellProfiler Analyst. This blog post will cover how to convert a spreadsheet into a database and make a usable .properties file with which to load it into CellProfiler Analyst.

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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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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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Browser-based Apps for Data Visualization

Minh Doan

Have you ever stumbled across some amazing data visualization tools that run entirely on a web browser (such as this and many others), and wished you could plug in your own data and visualize it? Or, as a biologist, you may know of a good analytic tool, but it either costs too much, requires programming expertise, or requires bundled installations of many other dependencies that might not be compatible...

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