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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 points are, and how easy it is to learn how to do any of this in the first place. While things like...

Pearl V. Ryder In the previous post in this “Thinking like an image analyst” series, I explained how I enhanced fibers to increase their brightness and applied a background subtraction to decrease the intensity of the background. In combination with masking out very bright debris pixels ( Part II of...

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Rebecca Senft Workflow update June 2024 update Our recommended normalization workflow is evolving. Please see https://github.com/broadinstitute/jump-profiling-recipe/ for our latest developments on the normalization strategy in specific and aprofiling workflow in general. How to Normalize Cell...

Segmentation is an integral step of any bioimage analysis workflow, which involves delineating areas or objects of interest within an image 1 . All the measurements performed on the image, e.g. size, shape, counts, or pixel intensities are then assigned to these segmented areas or objects to...

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Beth Cimini Happy holidays to everyone- we here at the CellProfiler team got you a little end-of-year treat in the form of CellProfiler 3.1.8. This is primarily a bugfix release, getting rid of some bugs in MeasureObjectIntensity, MeasureColocalization, ExportToSpreadsheet...

Beth Cimini I’m excited to announce the release of CellProfiler 3.1. Our focus for CellProfiler 3.1 was polishing features and squashing bugs introduced in CellProfiler 3.0. We also started laying down the foundation for our next release, CellProfiler 4.0, that will transition CellProfiler from...

Guest Author This post was written by a guest author, Kun-Hsing Yu, who can be reached at Kun-Hsing_Yu@hms.harvard.edu. Lung cancer causes more than 1.4 million deaths per year. To diagnose lung cancer, pathologists prepare microscopic slides from surgical or biopsy samples, stain them with...

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...