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

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 able to successfully segment the images that were not able to be accurately segmented by Pearl’s...

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

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 these methods were successful in accurately segmenting the fibers so I decided to develop a machine...

Help! How does the Robust Background method work?

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, since it contains the largest number of tunable parameters of any thresholding algorithm in CellProfiler, it...