In person trainings

Hi there, I was wondering if anyone had any in person trainings or tutorials for Cell Profiler and/or Analyst scheduled in the near future? Are there any events or conferences where more material might be presented on how to best use the software?
Thank you.

1 Like

@Anne_Carpenter Do you know the answer?

Hi there,
The CellProfiler team is short-staffed at the moment, so we are taking a break from hosting tutorials here in the Boston area. However, there is one upcoming in Seattle (Saturday, June 11, 2016):

Configuring Accurate Cell Detection in Images Using CellProfiler

Carolina Wählby, Uppsala University, Sweden
Lee Kamentsky, Broad Institute of Harvard and MIT, USA
Anne E Carpenter, Broad Institute of Harvard and MIT, USA

Object detection is the first and often most crucial step in any image based analysis approach when measurements are to be extracted from objects such as individual cells in an image. Robustness and accuracy of object detection depends on many factors, such as noise, variability in staining efficiency, clustering of objects, and background illumination variations. Automated image analysis approaches for object detection can be optimized in many different ways, and the number of different parameters that can be tweaked is often overwhelming. During this tutorial we will focus on algorithms and parameter settings for object detection in the free and open source CellProfiler software. We will go through thresholding and watershed segmentation, including different options for pre-processing, image enhancement and background illumination correction. We will also look at the details of separating adjacent cells based on shape and intensity. We will explain how the algorithms and settings are presented in CellProfiler, and discuss strategies for parameter optimization using a number of real examples. We will also discuss pixel classification as a pre-processing step for segmentation, and show how measuring objects is a simple task once objects are accurately detected.

After participating in this tutorial, the students should be able to approach their own image analysis challenges using CellProfiler, and have a good grasp on how to optimize settings for accurate object detection. They will also know how to extract and export measurements such as size, shape, position and counts of objects to quantitatively answer questions related to variations in cell morphology as observed by microscopy or image flow cytometry.

Thank you so much for your response! This definitely looks interesting.

Dear Shay,

You may try whether you can work yourself through my teaching material:

Normally I am around to teach this, but maybe it is possible to do it on your own.
In case you try, please let me know how it goes and how I could improve it.

Best, Christian


Hi Christian,

Thank you for the material! I will definitely take a look over it.