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In addition to JUMP Partners, JUMP Collaborators worked on limited parts of the project as a collaborative effort, to develop technologies, reagents, and methods. Administrative: Pistoia Alliance Academic: Umeå University Stanford Machine Learning Group

New public workflow available!

News: November 05, 2021

We are pleased to announce that our first publicly available bio image analysis workflow (an outcome of a collaboration with the Newmark lab at Morgridge Institute for Research) is now available via our COBA GitHub repository. This example workflow automatically detects, orders, and saves individual...

Thinking like an image analyst, Part V: Making measurements and exporting the data for analysis

Blog: November 12, 2021

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...

Published: "CellProfiler 4: improvements in speed, utility and usability"

News: September 10, 2021

BMC Bioinformatics published a paper by members of the COBA team detailing the release of CellProfiler 4. CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to...

Thinking like an image analyst, Part IV: Detecting fibers as objects

Blog: November 05, 2021

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...

Karen Mao

Person: Research Associate

Karen Mao, BSResearch Associate

Nodar Gogoberidze

Person: Principal Software Engineer

My background and education, through to my master's degree, has been centered at the intersection of Software Engineering and Data Science. I'm excited by the application of research and innovation in these domains towards slow, arduous, or otherwise intractable problems.

Anne Carpenter featured

News: November 02, 2021

COBA PI Anne Carpenter was featured in a 4 minute mini documentary video and article by Quanta magazine, where she shares her passion for bridging biology and computer science in the field of imaging.

Published: "CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis"

News: September 03, 2021

We have now released CellProfiler Analyst 3.0. Bioinformatics published a paper by members of the COBA team outlining the update. In addition to enhanced performance, this CellProfiler Analyst release adds support for neural network classifiers, identifying rare object subsets, and direct transfer...