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Hi all,

Due to issues with pip installation with CellProfiler on some platforms, we have released a version 4.2.6 with slightly updated dependency pins. If you are using the CellProfiler 4.2.5...

Microscopy in the cloud: CellProfiler and Cell Painting on Terra

Authors: Carmen Diaz Verdugo, Stephen Fleming, Nicole Deflaux and Amy Unruh

Carmen Diaz Verdugo is a Computational Scientist in the...

When you are new to the coding world, a lot of new information can be overwhelming. Staying organized might help ease the learning process. This blog post is about simple ways to organize your Jupyter...

Beth Cimini

In the Imaging Platform, we tend to work on a lot of big, complicated projects, with a lot of moving pieces and sometimes collaborators in many countries! This is fantastic for science...

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...