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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...

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...

Beth Cimini Hi all, We hope you’re enjoying our new CellProfiler 4.1 release! If you haven’t had a chance to see it yet, please do grab a copy from https://cellprofiler.org/releases. There are a few new features or changes of note we’re particularly excited to share with you all: For the first time...

David R. Stirling Hi all, We’ve now released CellProfiler 4.2! You can download it from https://cellprofiler.org/releases. We have a few new features and improvements in this release. There have been numerous smaller bug fixes, but the key changes are as follows: We’ve fixed an issue which was...

Pearl V. Ryder In the previous blog post in this series, I demonstrated how I masked out debris that was brighter than the fibers of interest. In this post, I’ll walk through how I enhanced the fibers in order to increase their brightness and decreased the background intensity of the images. If you...

Barbara Diaz-Rohrer If you are working with single-channel images, you can just drag a few images into CellProfiler and start making your pipeline. Most of us, however, have images with multiple channels or more complex image metadata that you need to tell CellProfiler how to identify.The tutorial...

Melissa Gillis Segmenting fibers using traditional cell segmentation software can be challenging. Because most biological cell segmentation tools were designed for cells, most programs have difficulty identifying and distinguishing longer and thinner objects such as fibers. Also, unlike cells...

When you are new to the coding world, a lot of new information can be overwhelming. Staying organized might help ease the learning process. This blog post is about simple ways to organize your Jupyter notebooks to make them more reproducible and user-friendly. First, let me begin by introducing the...

Microscopy in the cloud: CellProfiler and Cell Painting on Terra Authors: Carmen Diaz Verdugo, Stephen Fleming, Nicole Deflaux and Amy Unruh Carmen Diaz Verdugo is a Computational Scientist in the Precision Cardiology Lab, and a member of Patrick Ellinor’s group. Stephen Fleming is a Senior Machine...