Blog

Rebecca Senft

Let’s talk about normalization: why we normalize data and how we choose a method for normalizing data in Cell Painting experiments. We’ll consider a theoretical example experiment...

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...

by Erin Weisbart

This explains how to set up a Dashboard in Amazon Web Services (AWS) Cloudwatch, which widgets we find most helpful for monitoring Distributed CellProfiler (DCP) runs in our...

Pearl V. Ryder

In the previous posts in this series, I explained how I approached an image analysis project to segment extracellular fibrils, giving an overview of the project (Part I), showing how I...

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...

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...

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...

Pearl V. Ryder

One thing I’ve found very helpful in my journey as an image analyst is learning from others by observing their thought process when they tackle a new problem. In this series of five...

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...

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...