Carpenter Lab

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

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...

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...

Kyle Karhohs

# Sharing Image Data

At the Imaging Platform we frequently need to send and receive images between collaborators or forum users. Working with images can become challenging...

Guest Author

This post was written by a guest author, Kun-Hsing Yu, who can be reached at Kun-Hsing_Yu@hms.harvard.edu. 

Lung cancer causes more than 1.4 million deaths per year. To diagnose lung...

Anne Carpenter

Not every image you capture on your microscope is suited for quantification, no matter how nice they may look. Even though you might not notice any problems by eye, the tips outlined...

Kyle Karhohs

Now that CellProfiler can handle 3D images, how do you view the results? When processing 2D images, the IdentifyPrimaryObjects module will produce a figure that displays the original...

Kyle Karhohs

Joining forces

CellProfiler is capable of accurate and reliable segmentation of cells by utilizing a broad collection of classical image processing methods. Peruse the documentation on...

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...

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...

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...

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...

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

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

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 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 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...