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Press from the Imaging Platform (Carpenter-Singh and Cimini labs)

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Impact of CellProfiler on human health Our CellProfiler software has yielded discoveries in several translational projects, some of which may ultimately have a direct impact on the treatment of disease [ read more here]. Public videos of talks and PDF slides Links to PDFs of slides from recent talks...

Building a container image with Podman

Blog: February 05, 2026

Authors: Esteban Miglietta and Nodar Gogoberidze In a previous post, we have already discussed what Docker containers are and how to build them. Here, we're going to talk about an alternative to Docker for managing containers: Podman. But first... What are software containers? Software containers...

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...

Announcing CellProfiler 3.1.8

Blog: December 21, 2018

Beth Cimini Happy holidays to everyone- we here at the CellProfiler team got you a little end-of-year treat in the form of CellProfiler 3.1.8. This is primarily a bugfix release, getting rid of some bugs in MeasureObjectIntensity, MeasureColocalization, ExportToSpreadsheet...

Announcing CellProfiler 3.1

Blog: July 26, 2018

Beth Cimini I’m excited to announce the release of CellProfiler 3.1. Our focus for CellProfiler 3.1 was polishing features and squashing bugs introduced in CellProfiler 3.0. We also started laying down the foundation for our next release, CellProfiler 4.0, that will transition CellProfiler from...

Thinking like an image analyst, Part V: Making measurements and exporting the data for analysis

Blog: November 12, 2021

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...

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...

Compiling collaborators for NSF Collaborators and Other Affiliations (COA) form

Blog: November 08, 2024

Authors: Beth Cimini, John Kitchin, Andrew Rosen, and Anne Carpenter What is the COA form? NSF requires you to report all “Co-authors on any book, article, report, abstract or paper with collaboration in the last 48 months” in Table 4 of the COA form, for certain people (e.g. PI, Co-PI, Senior/Key...

Ksenija Krasina

Person: Senior 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...

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...