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  2. Help Series

Help! Why does CellProfiler say it can’t find any valid image sets?

January 09, 2017

Beth Cimini

Defining the input to CellProfiler can be the hardest part of getting your pipeline set up and your analysis underway.  Incoming images are configured in the first 4 modules of...

Read More Help! Why does CellProfiler say it can’t find any valid image sets?

Help! What are these three different modules to identify objects?

December 21, 2016

Beth Cimini

It can be confusing when you’re trying to set up your first pipeline to figure out which modules to use to generate your objects!  A helpful way to understand the difference between...

Read More Help! What are these three different modules to identify objects?

Help! I want to use CellProfiler Analyst but I ran my pipeline with ExportToSpreadsheet!

May 28, 2020

David R. Stirling

We’ve all done this before – CellProfiler Analyst needs a database file, but your CellProfiler pipeline that took days to run was set up to export spreadsheets. To make matters...

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Read More Help! I want to use CellProfiler Analyst but I ran my pipeline with ExportToSpreadsheet!

Help! How does the Robust Background method work?

August 05, 2021

Pearl V. Ryder

 

The Robust Background algorithm is a powerful algorithm for automatically setting thresholds to segment objects of interest when your image contains mostly background. However...

Read More Help! How does the Robust Background method work?

Customizing a Model for Fiber Segmentation, Part I: Investigating Possible Methods

August 05, 2022

Melissa Gillis

Segmenting fibers using traditional cell segmentation software can be challenging. Because most biological cell segmentation tools were designed for cells, most programs have...

Read More Customizing a Model for Fiber Segmentation, Part I: Investigating Possible Methods

Customizing a Model for Fiber Segmentation, Part 2: Creating an ilastik Model

August 05, 2022

Melissa Gillis

In the first part of this blogpost I described some of the tools I tried to accurately segment collagen IV fibers including, CellProfiler, Cellpose, and Piximi. Unfortunately none of...

Read More Customizing a Model for Fiber Segmentation, Part 2: Creating an ilastik Model

Customizing a Model for Fiber Segmentation, Part 3: Constructing a CellProfiler Pipeline

August 05, 2022

Melissa Gillis

In the previous two sections of this blogpost I explained how I analyzed multiple methods to segment fluorescent images of collagen IV fibers, and generated accurate segmentation using...

Read More Customizing a Model for Fiber Segmentation, Part 3: Constructing a CellProfiler Pipeline

Customizing a Model for Fiber Segmentation, Part 4: Analyzing the Results

August 05, 2022

Melissa Gillis

In the final section of this blogpost series, I will discuss some of the benefits and drawbacks of this model and discuss some of the data I acquired from the images.

This model was...

Read More Customizing a Model for Fiber Segmentation, Part 4: Analyzing the Results

Help! Interpreting image-based profiles

November 28, 2022

Fernanda Garcia-Fossa & Anne Carpenter

In a typical quantitative microscopy experiment, biologists choose fluorescent biomarkers and measure particular features (that is “metrics”) that they...

Read More Help! Interpreting image-based profiles
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