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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...

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 Cloudwatch Dashboard, and what you might learn from each widget. AWS Cloudwatch Dashboards are “customizable...

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 removed bright debris from the images (Part II), enhanced the fiber brightness and reduced...

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...

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...

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...

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 blog posts, my goal is to share how I approached an image analysis project that I recently undertook as...

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...

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...