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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.

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...

Software and code

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CellProfiler and CellProfiler Analyst Our lab previously launched and led the CellProfiler and CellProfiler Analyst projects, beloved by biologists around the world for bioimage analysis and cited over 15,000 times. They are now developed and maintained by the Cimini lab (since 2021). DeepProfiler ...

Ksenija Krasina

Person: 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...

Announcing CellProfiler 3.1.9

Blog: September 10, 2019

Beth Cimini Hello all! It’s been a crazy last few months for the CellProfiler team, as we’ve been hiring some new members to the team and working hard on the transition to Python 3, which will bump us into CellProfiler version 4. Keep your eyes peeled for exciting content in the future! We did want...

Tricks for maintaining your CV/resume with Google Docs: easy to edit, immediately published

Blog: September 19, 2018

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...

Annotating Images with CellProfiler and GIMP

Blog: June 07, 2018

Kyle Karhohs Annotated image data is valuable for assessing the performance of an image processing pipeline and as training data for machine learning methods such as deep learning. When assessing the performance of a CellProfiler pipeline, for example a pipeline that segments nuclei, the annotated...

CellProfiler 3.0 release: faster, better, and 3D

Blog: October 16, 2017

Anne Carpenter We are thrilled to announce that CellProfiler 3.0 is now released! Download it here. Eighteen months in the making, this is the first version of CellProfiler that can identify objects in 3D images volumetrically – the result of a collaboration with the Allen Institute for Cell Science...

Quantifying microscopy images: top 10 tips for image acquisition

Blog: June 15, 2017

Anne Carpenter Not every image you capture on your microscope is suited for quantification, no matter how nice they may look. Even though you might not notice any problems by eye, the tips outlined here for acquiring and storing images can improve the quality of data derived from digital image...