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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...

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. Whole slide file formats (e.g., .mrxs, .svslide, .svs, .vms) are often massive when uncompressed (>40 GB...

Fernanda Garcia-Fossa & Anne Carpenter In a typical quantitative microscopy experiment, biologists choose fluorescent biomarkers and measure particular features (that is “metrics”) that they hypothesize will be perturbed in their samples. But in image-based profiling, you aim to let the cells tell...

Pearl V. Ryder In the previous posts in this series, I explained how I approached an image analysis project to segment extracellular fibrils, giving an overview of the project (Part I), showing how I removed bright debris from the images (Part II), enhanced the fiber brightness and reduced...

Pearl V. Ryder In the first post of this series, I gave an overview of this project and explained how I imported the data into CellProfiler. If you’d like to follow along in CellProfiler, the pipeline and images for this project are available here. Now that the images have been imported, I could...

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. Separating the dyes into channels can be a difficult task with traditional methods such as split...

NEWS

Minh Doan Have you ever stumbled across some amazing data visualization tools that run entirely on a web browser (such as this and many others), and wished you could plug in your own data and visualize it? Or, as a biologist, you may know of a good analytic tool, but it either costs too much...

Beth Cimini For those of you who’ve been with us for a long time though, the obvious next question after how to use the new test mode is will my old CellProfiler pipelines work in the new version? We feel the same way – the pipelines you’ve accumulated over the years are precious resources! The good...

Kyle Karhohs Now that CellProfiler can handle 3D images, how do you view the results? When processing 2D images, the IdentifyPrimaryObjects module will produce a figure that displays the original image next to the segmented image to make validation fast and convenient, a side-by-side comparison...