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Thinking like an image analyst, Part II: Removing bright debris from analysis

Blog: August 17, 2021
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...

UnmixColors Modules Tutorial

Blog: July 22, 2022
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. Separating the dyes into channels can be a difficult task with traditional methods such as split...

NSF BBSRC Imaging Flow Cytometry Project

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NSF BBSRC Imaging Flow Cytometry Project (July 15, 2015–June 30, 2018) [ Project abstract at nsf.gov] [Project Outcomes Report (search here, using Fed Award ID 1458626 ( PDF))] Non-technical description of the problem: There are a variety of cell types circulating in human blood, each with distinct...

Promo Images

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Biographical images are available here with credits noted in each folder name. Permission to use those or any images on this page must be requested via imagingadmin@broadinstitute.org.

Ksenija Krasina

Person: Imaging Platform Administrative Assistant
I am the Administrative Assistant for the Imaging platform, holding dual master’s degrees in Digital Economy and Business from Zagreb University of Applied Sciences, as well as Cultural and Fashion studies from the University of Zagreb. My interests lie in the financial aspect of nonprofit...

Ankur Kumar

Person: Computational Associate II
I am interested in hacking biological systems for fun and profit. This includes (non-exhaustively) using tools from mathematics, computer science, and engineering disciplines to probe, understand, and program biological systems.

Software and code

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DeepProfiler DeepProfiler is a set of tools that allow you to use deep learning for analyzing imaging data in high-throughput biological experiments. Documentation and instructions for DeepProfiler can be found in our Handbook and the code is located on the GitHub page. Cytominer The Pycytominer...

Help! How does the Robust Background method work?

Blog: August 05, 2021
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, since it contains the largest number of tunable parameters of any thresholding algorithm in CellProfiler, it...

Getting started using CellProfiler from the command line

Blog: April 30, 2021
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...

Announcing CellProfiler 4.2.6 and RunCellpose updates

Blog: August 16, 2023
Hi all, Due to issues with pip installation with CellProfiler on some platforms, we have released a version 4.2.6 with slightly updated dependency pins. If you are using the CellProfiler 4.2.5 application downloaded from our website, there is no need for you to update - 4.2.6 contains no changes to...