NimbusImage

NimbusImage is an open source image analysis platform for researchers in the life sciences

Imaging has led to major discoveries in the life sciences. With the advent of powerful imaging techniques and microscopes, we are now awash in data. However, analyzing this heterogeneous data—at scale, with accuracy and reproducibility—has proven to be a major challenge.

We have developed NimbusImage as a platform to empower scientists to analyze their image data and spend their time making discoveries rather than struggling to process their datasets.

NimbusImage is…

• Geared towards life sciences. Our target audience is cell biologists who work with microscopy data. Our focus has been fluorescence microscopy, but are keen to expand to serve more communities over time.

• Web-based. NimbusImage lives in the cloud and requires no installation. It can handle very large datasets without worrying about local storage and memory. NimbusImage enables fast and easy data sharing and analysis.

• Scalable. NimbusImage was designed from the ground up to handle the viewing and analyzing of large datasets. As microscopes have become capable of producing ever-increasing amounts of data, even just loading datasets can be a challenge. NimbusImage enables interaction with big datasets in the browser.

• Open source. NimbusImage is built in the open. Anybody can run their own image server. All the code is open for scrutiny.

• Fun. Image analysis is often a painful, mind-numbing task. We hope that NimbusImage will spark joy as you interact with your beautiful data.

What is special about NimbusImage?

NimbusImage has a slightly different approach to image analysis than other tools. Most approaches to image analysis are built around pipelines, where you set a bunch of parameters, run a big dataset through the algorithms, and then end up with some numbers in a table. What is typically missing is the ability to visualize and interact with your analysis. For instance, maybe some region was out of focus and you want to exclude it. Or some spots were assigned to the wrong cell. Or some cell segmentation needs to be cut in half. NimbusImage allows you to use cutting-edge algorithms and interact directly with the output, making sure your analysis reflects your data accurately and injecting your knowledge and intuition back into your work.

NimbusImage has been developed by the lab of Arjun Raj at the University of Pennsylvania, a Professor in the Department of Bioengineering and the Department of Genetics (major contributions from William Niu) in collaboration with Kitware, a company whose mission is to make open-source platforms for science and makers of ITK and Girder.