Workshop on quantitative automated analysis of microscopy data using CellProfiler


This national workshop is organized by the SciLifeLab BioImage Informatics national facility. It is open for PhD students, postdocs, researchers and other employees in need of image analysis skills within all Swedish universities.

Registration and course fee

Please contact Petter Ranefall at petter.ranefall@scilifelab.uu.se to register for the workshop. Please note that the workshop is limited to 18 participants; first come first serve.

The workshop is free of charge.

Course content

CellProfiler is free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler is developed and supported by the Broad Institute of Harvard and MIT. The workshop will be very practical, and all participants are asked to download (www.cellprofiler.org) bring their own laptops (mac or PC) and install CellProfiler prior to the workshop. The first half of the day will be focused on how to get started and how to set up your own pipeline for automated analysis. After the lunch break we will also provide hands-on help for getting started setting up pipelines for analysis of the participants’ own data, and for those interested describe how the tools can be used for high-throughput screening using CellProfiler Analyst.

Teachers

Beth Cimini – Lead Assay Developer @Broad Institute of MIT and Harvard, US

Carolina Wählby – Professor at the Dept. of IT, Uppsala University and Director of the Uppsala site of the SciLifeLab BioImage Informatics platform

Kevin Smith – Associate Professor at KTH Royal Institute of Technology and Director of the Stokholm site of the SciLifeLab BioImage Informatics platform

Petter Ranefall – Associate Professor at the Dept. of IT, Uppsala University and Head of the Uppsala site of the SciLifeLab BioImage Informatics platform

Venue

Husargatan 3, Uppsala (BMC entrance C11)
Room 4308, 4th floor SciLifeLab Navet.