Center for Bio-Image Informatics

Engineering, Biology and Computer Science, working together.

  • Increase font size
  • Default font size
  • Decrease font size

2008 - Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining

E-mail Print PDF
Workshop on BioImage Informatics at UCSB

UCSB, Santa Barbara, CA, USA, January 17-18, 2008

Go to the workshop homepage.

This NSF sponsored workshop brought together over 150 researchers who work at the intersection of bioimaging and image informatics. Participants presented interesting and significant results from their research efforts in the study of biological processes. The research presented spanned a broad range of disciplines, including image data analysis, computer vision, data mining, machine learning, visualization, and informatics.Overall the workshop was a great success and facilitated the cross-polination of research ideas from different Bio-Imaging research laboratories around the world. Submissions were way up on last year, with a total of 55 submissions overall, including 23 oral presentations with 7 invited talks and 2 keynote speakers.

Presentation videos and photos are available in the full article.

There were 32 poster presentations on display in two specific poster sessions and throughout the workshop. Attendance was high on both days of the workshop and rich discussion followed every presentation that was delivered. The workshop concluded with a lively discussion panel consisting of a range of perspectives from prominent researchers on the salient issues of standardization and the establishement of reliable benchmarks within bio-imaging and its associated fields. These perspectives addressed the need for high quality, reliable test datasets for validation of image processing and analysis algorithms. The discussion panel was chaired by Jitendra Malik, UC Berkeley and Maryann Martone, UCSD. The panel consisted of Mark Ellisman (UC Berkeley), Anne Carpenter (Broad Institute of Harvard and MIT), Jonathon Phillips ( National Institute of Standards and Technology) and Ilya Goldberg (National Institute of Health). The discussion was contributed to by a large number of questions and comments from the audience.

Full presentations:

Placeholder for Flash player

 

SESSION 1

[VID] Keynote Talk
Scott Fraser, CalTech
[DOWNLOAD MPEG4] 341M

SESSION 2

[VID] Invited talk: "On the construction and analysis of patient-specific models from medical images"
Eric Grimson, MIT
[DOWNLOAD MPEG4] 256M
[VID] "Computer-assisted Histopathology: Experience with Neuroblastoma and Follicular Lymphoma"
Metin Gurcan, Ohio State University
[DOWNLOAD MPEG4] 93M
[VID] "Turning Images into Knowledge: Cognition Network Technology for the Analysis of Life Sciences Image Data"
Colin Blackmore, Definiens AG
[DOWNLOAD MPEG4] 136M

SESSION 4

[VID] Invited talk: "Molecular Phenotype Atlases: Motivation, Challenges and Workflow"
Robert Marc, Utah
[DOWNLOAD MPEG4] 245M
[VID] "Computational Neuroanatomy from Genome Scale Gene Expression Data in the C57Bl/6J Mouse Brain"
Michael Hawrylycz, Allen Institute for Brain Science
[DOWNLOAD MPEG4] 137M
[VID] "Berkeley Drosophila Transcription Network Project: Morphology and Gene Expression Atlas"
Cris L. Luengo Hendriks, Lawrence Berkeley National Laboratory
[DOWNLOAD MPEG4] 101M
[VID] "Morphomic Analysis of a Simple Chordate"
Michael Veeman, UCSB
[DOWNLOAD MPEG4] 121M

SESSION 6

[VID] Invited talk: "The Open Microscopy Environment: Open Image Informatics for Biological Microscopy"
Jason Swedlow, University of Dundee
[DOWNLOAD MPEG4] 189M
[VID] "Bisque: Bio-Image Semantic Query User Environment"
Kristian Kvilekval, UCSB
[DOWNLOAD MPEG4] 136M
[VID] "Selective Scanning for faster Prostate Pathology"
Mayank Kabra, U.C. San Diego
[DOWNLOAD MPEG4] 102M
[VID] "Automated quantitative analysis of phenotype similarities"
Eckley, D. M.
[DOWNLOAD MPEG4] 113M

SESSION 7

[VID] Keynote: "Multiscale Imaging of the Nervous System"
Mark Ellisman, UCSD
[DOWNLOAD MPEG4] 365M

SESSION 8

[VID] Invited talk: "Managing uncertainty in bioimage databases"
Ambuj Singh, UCSB
[DOWNLOAD MPEG4] 161M
[VID] Invited talk: "Evaluations and benchmarking: transitioning from biometrics to bioimaging"
Jonathon Phillips, NIST
[DOWNLOAD MPEG4] 184M
[VID] "Analysis of Intravital Microscopic Images of Rolling Leukocytes"
Scott T. Acton, University of Virginia
[DOWNLOAD MPEG4] 109M

SESSION 9

[VID] Invited talk: "Single cell analysis of drug perturbations"
Steve Altschuler, UT Southwestern Medical Center
not available
[VID] "Automatic Segmentation of Microtubule Plus End Motion into Phases of Growth and Shortening"
Stathis Hadjidemetriou, Yale University
[DOWNLOAD MPEG4] 77M
[VID] "Multivariate characterization of membrane proteins"
Bahram Parvin, Lawrence Berkeley National Laboratory
[DOWNLOAD MPEG4] 95M

SESSION 10

[VID] Invited talk: "Gene module discovery by cytological profiling of RNAi-perturbed cells"
Anne Carpenter, Broad Institute
151M
[VID] Invited talk: "GoFigure and The Digital Fish Project: Open tools and open data for an imaging based approach to systems biology"
Alexandre Gouaillard
[DOWNLOAD MPEG4] 130M

SESSION 11

[VID] PANEL: "Benchmarking and validation of computer vision methods for bioimages"
Panelists: Goldberg, Ellisman, Carpenter, Phillips
[DOWNLOAD MPEG4] 161M