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UnmixColors Modules Tutorial

Mario Costa Cruz If you have color images stained with light-absorbing dyes, the UnmixColors module might be able to separate the dyes into separate channels so that they can be analyzed separately. Separating the dyes into channels can be a difficult task with traditional methods such as split...

How to Normalize Cell Painting Data

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 including two plates, each with a different cell type (neurons and fibroblasts). Plates include similar...

Input Modules Tutorial

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...

Community’s Input: 2020 BioImage Analysis Survey

Nasim Jamali As creators of open source tools, we spend a lot of time thinking about user needs - what kinds of images people are working with these days, what tools are working well, where the pain points are, and how easy it is to learn how to do any of this in the first place. While things like...

Creating a Cloudwatch Dashboard to Monitor Distributed CellProfiler Runs

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...

Thinking like an image analyst, Part IV: Detecting fibers as objects

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...

Thinking like an image analyst, Part III: Enhancing fibers for detection

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...

New CellProfiler 4 Plugin: RunCellpose

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...

Thinking like an image analyst, Part II: Removing bright debris from analysis

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...