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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 Precision Cardiology Lab, and a member of Patrick Ellinor’s group. Stephen Fleming is a Senior Machine...

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, but when it comes to writing a paper, it can make just gathering all the information about "who did...

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...

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...

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 objects or measuring the things I care about?” Unfortunately, it’s also one of the hardest questions to...

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 vitae (CV), all updated and ready to go. But, if you’re like most academics, your CV is a sorely outdated...