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Fernanda Garcia-Fossa & Anne Carpenter

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

Rebecca Senft

With slide scanners and other automated, high-throughput microscopes becoming more and more common, it’s important to understand how to work with the large image files they produce...

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...

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...

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...

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...

Mario Costa Cruz

If you have color images stained with light-absorbing dyes, the UnmixColors module might be able to separate the dyes into separate channels so that they can be analyzed separately.

Rebecca Senft

Let’s talk about normalization: why we normalize data and how we choose a method for normalizing data in Cell Painting experiments. We’ll consider a theoretical example experiment...

Barbara Diaz-Rohrer

If you are working with single-channel images, you can just drag a few images into CellProfiler and start making your pipeline. Most of us, however, have images with multiple...

Nasim Jamali

As creators of open source tools, we spend a lot of time thinking about user needs - what kinds of images people are working with these days, what tools are working well, where the pain...