How-To

Segmentation is an integral step of any bioimage analysis workflow, which involves delineating areas or objects of interest within an image¹. All the measurements performed on the image, e.g. size...

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...

When you are new to the coding world, a lot of new information can be overwhelming. Staying organized might help ease the learning process. This blog post is about simple ways to organize your Jupyter...

Rebecca Senft

With slide scanners and other automated, high-throughput microscopes becoming more and more common, it’s important to understand how to work with the large image files they produce...

Melissa Gillis

In the final section of this blogpost series, I will discuss some of the benefits and drawbacks of this model and discuss some of the data I acquired from the images.

This model was...

Melissa Gillis

In the previous two sections of this blogpost I explained how I analyzed multiple methods to segment fluorescent images of collagen IV fibers, and generated accurate segmentation using...

Melissa Gillis

In the first part of this blogpost I described some of the tools I tried to accurately segment collagen IV fibers including, CellProfiler, Cellpose, and Piximi. Unfortunately none of...

Melissa Gillis

Segmenting fibers using traditional cell segmentation software can be challenging. Because most biological cell segmentation tools were designed for cells, most programs have...

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.

Rebecca Senft

Workflow update

June 2024 update 

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...

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...

Guest Author

This post was written by a guest author, Jillian Rowe, who can be reached at jillian@dabbleofdevops.com. 

Running CellProfiler in batch mode is the ideal way to automate large...

Minh Doan

Have you ever stumbled across some amazing data visualization tools that run entirely on a web browser (such as this and many others), and wished you could plug in your own data and...

Kyle Karhohs

Annotated image data is valuable for assessing the performance of an image processing pipeline and as training data for machine learning methods such as deep learning. When...

Beth Cimini

Everyone here at the CellProfiler team is very excited about our new 3.0 release, and we certainly hope you are too!  CellProfiler 3.0 is much faster than any of our previous releases...

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...