Show threadBeth Cimini 🔬💻📊Apr 7, 2025
Our first two episodes (on handling out of focus regions in images, as well as on how to download data from the IDR) are available now, with new episodes will drop ~every two weeks(ish)! While it will heavily feature #CellProfiler, we will use whatever tool is right for the challenge. (2/x)
Bluesky

Bluesky Social
AdriftLabMay 23, 2023

Brilliant final seminar by our phenomenal #AdriftLab student, Gabbi and her superb team of supervisors 🥳👏

Gabbi looked at how we can more accurately & efficiently define #plastic #colour. How the #plastics community currently reports colour is hugely problematic (very ad hoc). Stay tuned for our free, user-friendly tool to streamline your #PlasticPollution workflow.

#CellProfiler #TeamWork #ThesisSubmission #MethodDevelopment #StandardiseReporting #PlasticIngestion #Seabirds #BeachPlastic @SeabirdSentinel @TheLabAndField @Jobium

Corentin Cras-MéneurMay 9, 2023
Why didn’t-I use Cell Profiler (https://cellprofiler.org) before?? The app works great for counting nuclei, colocalization etc. Really impressed. I used to do the same things in FIJI, but this is much faster (and still pretty easy) than whatever ImageJ plugins I was using there.
#CellProfiler #Microscopy #Imaging #Morphometry
CellProfiler

Free open-source software for measuring and analyzing cell images.

Hoang Anh Le (aka Anh), PhDFeb 7, 2023
I have this silly question about #imagesegmentation. So is there any advantage to using different software for image segmentation? I see #ImageJ, #CellProfiler, #Napari and #Python all can do this, but if the underlying algorithm is the same, then why not just stick with ImageJ?
Beth CiminiJan 11, 2023
Looking to learn more about #bioimageanalysis in 2023? Reminder that every other Friday (including this Friday), the #CellProfiler team hosts
Center for Open Bioimage Analysis (openbioimageanalysis.org) Office Hours! Signups can always be found at https://broad.io/imagingofficehours
CellProfiler Office Hours - January 13, 2022

Come ask us your image analysis questions! The CellProfiler team at the Broad Institute is hosting bi-weekly virtual office hours where you can sign up for a 30-minute time slot to work one-on-one with an assay developer to help solve image analysis problems! It is expected that prior to making an appointment for office hours, you first post your question at forum.image.sc. If you're still unable to get the help you need, office hours may be a good fit. One-on-one office hours are designed to help you develop your pipeline or make your existing pipeline better, so please make sure you have images available to share, when possible. You may sign up for two slots per year. Office hours will be held via Zoom conferencing and the link will be sent to the email address you provide here. Please review the available slots below (all times Eastern USA) and click on the button to sign up. Office hours are sponsored by COBA (nihcoba.org). The Center for Open Bioimage Analysis (COBA) should be acknowledged in any publications arising from data analysis or software development with COBA using the following text: "The experiments reported in this paper were performed in collaboration with the Center for Open Bioimage Analysis (COBA) which is supported by National Institute of General Medical Sciences NIH P41 GM135019."

Google Docs
Show threadashish(@tp53)Dec 16, 2022
@bethcimini thanks for putting it out ! I am a newbie bioinformatician with very little biology knowledge , and have been greatly inspired by @DrAnneCarpenter work on #CellProfiler and it's impact on drug discovery at Recursion, and wanting to learn about microscopy and imaging. Does this primer assume some biology knowledge as a prereq ?
Albert CardonaNov 25, 2022

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.

#java #python #kotlin #groovy

Show threadAnne CarpenterNov 18, 2022

#Introduction Part 2:
My lab invented the open-source software CellProfiler and the imaging assay Cell Painting and we now focus on using our machine learning and deep learning skills for image-based profiling, to accelerate drug discovery and functional genomics. Our research led to the founding of Recursion, a clinical-stage techbio powered largely by the information in cell images.

#CellProfiler #DrugDiscovery #TechBio #RXRX #MachineLearning #DeepLearning

Albert CardonaNov 6, 2022

Have you discovered the image processing forum yet? https://forum.image.sc

Featuring tutorials, requests for guidance, help, discussion of new features and documentation for open source software #FijiSc #ImageJ #CellProfiler #DeepLabCut #Icy #ilastik #napari #QuPath #scikitimage #StarDist and many more.
#java #python #kotlin #groovy