We are co-organizing a computational challenge at the ICLR 2022 workshop of geometry and topology. The goal is to push forward the field of computational differential geometry by asking participants to contribute statistics and learning algorithms on manifolds. The guidelines of the challenge can be found on its GitHub repository. The deadline is April 4th, 2022. Would you know people who could be interested in participating in the challenge? It can be a good opportunity... Read more
BisQue 2 has recently launched with a beta release! This new version of BisQue has a new storage backend and fully runs on Kubernetes. Active BisQue users should begin migrating any data stored on BisQue to BisQue 2, as BisQue will eventually be deprecated.
Despite vaccines being readily available for almost every age group, Covid-19 still remains a fatal disease if not detected early enough. As such, two Covid-19 detection modules are making their way to BisQue's cloud platform in the near future. One module will perform processing and classification on 3D lung CT scan volumes to determine if a patient is healthy, has Covid-19, or has pneumonia. The other detection module will analyze chest X-rays and output bounding boxes around abnormalities found in the X-rays.  
Normal Pressure Hydrocephalus (NPH) is a disorder in which ventricles in the brain swell from an accumulation of excess cerebrospinal fluid. This disorder can lead to difficulty in walking, thinking, and other daily functions. Like Alzheimer's and Parkinson's disease, NPH affects the elderly but is often misdiagnosed. As such, a NPH detection module has been integrated into the BisQue cloud platform. This module performs image segmentation on brain CT scans to locate and identify the volume of brain ventricles and ultimately provide a fast method to properly diagnose multitudes of patients.
The BioShape lab has been awarded an NIH R01 grant for biological shape reconstruction. The lab aims to introduce geometric and deep learning methods to enhance 3D biological shape reconstruction. Collaborators: Cornelius Gati - University of Southern California Khao Dao Duc - University of British Colombia Frédéric Poitevin - Stanford SLAC Claire Donnat - University of Chicago... Read more
BisQue has now moved its entire orchestration system to align with the latest software trends for distributed systems. With the move to Kubernetes, BisQue is now highly available (fault tolerant) and scalable across multiple nodes. We achieved this by taking advantage of the Kubernetes control loop that constantly checks the defined state of our deployment. If any of our pods or nodes fail, resources are rescheduled automatically to match BisQue’s desired state. GPU nodes are now labeled and can have jobs that require GPU resources scheduled on those nodes without any manual interaction. This... Read more
An accurate 3D cell segmentation module utilizing a 3D U-Net based neural network, a 3D watershed algorithm applied to a probability map, and CRF refinement has been integrated into the BisQue cloud platform.
UCSB researchers given the award from NSF’s Office of Advanced Cyberinfrastructure to build a large-scale distributed image-processing infrastructure (LIMPID) through a broad, interdisciplinary collaboration. Encompassing databases, image analysis and various scientific disciplines, their creation, BisQue, is an image informatics platform that shares, distributes and collaborates with large image datasets. “Think of BisQue as Google Docs for scientific images,” said UCSB principal investigator B. S. Manjunath, who directs the campus’s Center for Multimodal Big Data Science and Healthcare. “... Read more
The center we will be hosting the second LIMPID/BisQue workshop on Scalable Image Informatics. This is a joint meeting with the workshop on Applications of Machine Learning and Scalable Image Informatics to Materials Discovery, held as part of the NSF-sponsored IDEAS program on Data-Driven Approaches to Materials Discovery, at the University of California at Santa Barbara. Participation is by invitation only and we are expecting over 80 registered participants. The three day joint workshop will take place at UCSB from February 3-5, 2020. The workshop will start at 8:00 AM on Monday, February... Read more