Cell profiler

Trainer: Beth Cimini

Overview: CellProfiler is an open source image analysis tool allowing users to create a reproducible workflow that can be scaled to a single image or >1 million images. This session will cover how to tune object segmentations in CellProfiler based on principles of computer vision, how to use CellProfiler to create large measurement suites, and how to set up CellProfiler to run on large sets of images.

Learning outcomes

By the end of this session you will be able to:

• Explore the application of CellProfiler
• Identify the functionalities of the CellProfiler software

Materials:

• Presentation slides
• Web page

CellProfiler – Practical

Trainer: CellProfiler team

Overview: For this exercise, find subset of the data from idr0036 (https://idr.openmicroscopy.org/webclient/?show=screen-1952) and apply CellProfiler for analysis. You will gain experience tuning a pipeline that can cope with not only different cell phenotypes but also images of empty wells, blurry wells, debris, and other real-world potential screen confounders.

Materials:

• CellProfiler
• idr0036 – Public data for images
• GitHub version of the data – Find useful tutorials and pipeline at this GitHub page.