General Knowledge

Microscopy in the cloud: CellProfiler and Cell Painting on Terra

Authors: Carmen Diaz Verdugo, Stephen Fleming, Nicole Deflaux and Amy Unruh

Carmen Diaz Verdugo is a Computational Scientist in the...

Beth Cimini

In the Imaging Platform, we tend to work on a lot of big, complicated projects, with a lot of moving pieces and sometimes collaborators in many countries! This is fantastic for science...

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...

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...

Beth Cimini

One of the most common questions I’m asked when helping a collaborator with an image analysis project is:

“How do I know when my analysis workflow is doing well enough at finding the...

Jeanelle Ackerman

You’ve earned degrees, authored papers, mentored supervisees, and traveled far and wide to speak about your work… And ideally it’s nicely showcased in your resume or curriculum...

Anne Carpenter

As the PI of the Carpenter lab (a.k.a. Broad Institute Imaging Platform, including the CellProfiler team), people often ask how I manage so many ongoing collaborations: we discuss...

Beth Cimini

Double clicking on the output images produced by CellProfiler sometimes opens up a screen in your operating system’s default image viewer that looks all black. This can make it seem...

Minh Doan

Thanks to the rapid advancement in image processing, we now have so many techniques to characterize cellular and subcellular objects (hooray CellProfiler!) Measuring cultured cells in...

Beth Cimini

Defining the input to CellProfiler can be the hardest part of getting your pipeline set up and your analysis underway.  Incoming images are configured in the first 4 modules of...

Anne Carpenter

So you already know how to put together an image analysis pipeline to measure particular phenotypes of interest? Great!

Have you ever considered looking for the unexpected? Say you...