Search

Pearl V. Ryder In the first post of this series, I gave an overview of this project and explained how I imported the data into CellProfiler. If you’d like to follow along in CellProfiler, the pipeline and images for this project are available here. Now that the images have been imported, I could...

NEWS

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...

NEWS

Pearl V. Ryder The Robust Background algorithm is a powerful algorithm for automatically setting thresholds to segment objects of interest when your image contains mostly background. However, since it contains the largest number of tunable parameters of any thresholding algorithm in CellProfiler, it...

Beth Cimini Cross posted from our GitHub wiki — check there for any future updates! Running CellProfiler from the command line has a major advantage — you don't need to spend computational power or memory creating the graphical user interface (GUI) that you're used to using in CellProfiler! It also...

Pearl V. Ryder In the previous post in this “Thinking like an image analyst” series, I explained how I enhanced fibers to increase their brightness and applied a background subtraction to decrease the intensity of the background. In combination with masking out very bright debris pixels ( Part II of...