Search

David R. Stirling Hi everyone, Today we’re releasing the RunCellpose plugin for CellProfiler 4! This plugin is designed to allow you to use the popular Cellpose segmentation algorithm to generate object sets within a CellProfiler pipeline. Cellpose uses a neural network followed by post-processing...

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...

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...

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...

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 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...

Docker is discussed in the bioimage analysis world a lot these days. But what are dockers? How does Docker make life easier? In this blog post, I will try to explain the basics of docker and why it matters to biologists. Have you ever faced package dependency issues when creating Python environments...