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CellProfiler 4.0 Release: Improvements in speed, utility, and usability

Blog: September 09, 2020

David R. Stirling We have now released CellProfiler version 4.0! Download it here. The primary goal of this release has been to migrate CellProfiler from Python 2 to Python 3. This has involved extensive restructuring of the code base, leading to a lot of “under-the-hood” improvements. Important...

Thinking like an image analyst, Part I: Project overview and data import

Blog: August 10, 2021

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...

Creating a Cloudwatch Dashboard to Monitor Distributed CellProfiler Runs

Blog: December 01, 2021

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...

Alán Fernando Muñoz González

Person: Postdoctoral Associate

My interests lie in the interface of computer science, math, image analysis, and biology. I aim to develop tools and workflows to process high throughput imaging datasets, with special interest on applying computational methods on live microscopy data. I am also keen on extracting biological...

Research

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Our main research theme is quantifying and mining the rich information present in cellular images to yield biological discoveries, often using deep learning. We work on high-throughput projects (100,000-1,000,000 images) probing a variety of biological processes and diseases of interest, with a...

Contact

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Email imagingadmin@broadinstitute.org Mailing address Broad Institute of MIT and Harvard415 Main StreetCambridge, MA 02142Our offices are on the 5th floor of 415 Main St [ Google Maps link]. Look for the entrance of our building to the right of the Broad Institute sign.

NSF CAREER project page

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NSF CAREER Award Project (March 2012–February 2017) [ Project abstract at nsf.gov] [Project Outcomes Report (search here, using Fed Award ID 1148823 ( PDF))] Non-technical description of the problem: Biologists want to test genetic and chemical treatments in environments that more closely mimic the...

Jessica Ewald

Person: Postdoctoral Associate

I am interested in trying to predict and gain insights into adverse health outcomes in living organisms from rich cellular profiling data collected from in vitro experiments.

Anne E. Carpenter

Person: Principal Investigator, Institute Scientist, Senior Director of the Imaging Platform

Group Alumni

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Where are they now? Check their career progress on Dr. Carpenter's [ CV] Note: the Carpenter lab became the Carpenter-Singh lab in 2021. Alum Years Role Adam Fraser 2008–2011 Lead software developer for the CellProfiler Analyst project Adam Papallo 2005–2007 Bioinformatics Analyst Adeniyi Adeboye...