BisQue Deep Learning Cyberinfrastructure

(NSF CSSI-241153)

Bio-Image Semantic Query User Environment — store, visualize, organize, and analyze images in the cloud.

BisQue is an open-source platform for managing, exploring, and analyzing large-scale scientific multimodal data. BisQue combines images with structured metadata, annotations, sensor and experimental measurements, derived data products, models, workflows, and provenance. Its scalable web-services architecture supports data organization and search, interactive visualization, distributed storage, high-throughput analysis, and reproducible execution across diverse scientific domains.

Overview

  • Free and open-source

  • Support for large-scale imaging and associated multimodal scientific data

  • Flexible textual, graphical, and structured metadata annotations

  • Cloud scalability to petabytes of data and millions of annotations

  • Distributed storage through local systems, iRODS, and S3

  • Integrated, high-throughput AI/ML and scientific analysis workflows

  • Reproducible execution with workflow and provenance tracking

  • Analysis modules implemented in MATLAB, Python, Java, and ImageJ

  • Support for more than 100 scientific image formats

  • Interactive access to very large multidimensional images

Documentation & Source Code

The official documentation covers the BisQue cloud service running live at UCSB, module development for the platform, and the BQAPI. If you have any questions, feel free to reach out. We continuously update the documentation, so check back often for updates.

Official Documentation Try BisQue Now Source Code on GitHub

Related Papers

  • 2019Latypov, M.I., Khan, A., Lang, C.A. et al. Integr Mater Manuf Innov 8: 52. DOI →
  • 2019Polonsky, A.T., Lang, C.A., Kvilekval, K.G. et al. Integr Mater Manuf Innov 8: 37. DOI →
  • 2018Trigkakis D., Todorovic S., Preece J., Meier A., Elser J., Jaiswal P., Kvilekval K., Fedorov D., Manjunath B.S. PDF →
  • 2017D.V. Fedorov, K.G. Kvilekval, B.S. Manjunath, B. Doheny, S. Sampson, R.J. Miller. PDF →
  • 2016D. Fedorov, R.J. Miller, K. Kvilekval, B. Doheny, S. Sampson, B.S. Manjunath. View →
  • 2016J. Preece, J. Elser, P. Jaiswal, K. Kvilekval, D. Fedorov, B.S. Manjunath, R. Kitchen, X. Xu, D. Trigkakis, S. Todorovic, S. Carbon. PDF →
  • 2010Kvilekval K, Fedorov D, Obara B, Singh A, Manjunath BS. Bioinformatics 26(4):544–52 (PMID: 20031971). DOI →

Contact

Amil Khan
amil [at] ucsb [dot] edu
Connor Levenson
clevenson [at] ucsb [dot] edu
Chandrakanth Gudavalli
chandrakanth [at] ucsb [dot] edu
B.S. Manjunath (PI)
satish [at] ucsb [dot] edu