Category Archives: Website

General website info

VFB 2.0 beta release

We are proud to announce the release of VFB 2.0_beta1 designed in collaboration with MetaCell using the Geppetto open source platform. This release, available at https://v2.virtualflybrain.org, features:

  • An integrated 3D image browser that synchronises with the stack browser familiar from VFB 1.5
  •  

    A redesigned stack browser with fast section scrolling controlled by mouse-wheel or trackpad.

  •  A stylish new look and feel with an internal windowing environment and rapid synchronisation between components.
  •  A redesigned query interface making queries clearer and more easily extendable.

VFB 2.0_beta1 does not have the full functionality of VFB 1.5. In particular queries of FlyBase annotations of expression and phenotypes are not yet integrated. We are currently working on tuning queries for these and plan to incorporate them into the next release, scheduled for the end of April.

We’re also very busy adding new data including:

  • a new template for the larval CNS with painted domains and registered neurons
  • re-imaged VT lines from Janelia
  • split-GAL4 line images from FlyLight (Janelia)
  • neuron reconstructions from EM data

We are very keen to get community feedback on this release – including bug reports, features requests or just general suggestions. Please use the feedback link on the new site or email us on support@virtualflybrain.org.

Please note that although new development is focussed on VFB 2.0, we will continue to maintain VFB 1.5 in parallel.

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Filed under New Content, New Feature, Website

WEBINAR: Exploring the brain of a fly

Title
Neuroscience is advancing at a tremendous pace: the generation of circuit level hypotheses is experiencing an accelerated growth and it is now accompanied by an unprecedented ability to visualise, manipulate and record from individual neurons, in vivo. In this webinar, you’ll learn about the latest technological advancements in how disparate, large-scale datasets can be integrated, visualized and linked to a knowledge base and curated literature in the context of the brain of the Drosophila. MetaCell, world leaders in software for neuroscience, is hosting a free, open webinar to present Virtual Fly Brain, a unique resource for Drosophila neuroscience to produce fly brain data-driven imaging, visualization and browsing, ultimately providing the data to generate circuit hypotheses and identify research tools to test them. VFB is a joint effort of the University of Cambridge, University of Edinburgh and EMBL-EBI – funded by the Wellcome Trust. With exceptional guest speakers from the Virtual Fly Brain project, you’ll learn how you could make the most of your neuroscience imaging data and use your browser to explore the anatomy and the intricate relationships inside a brain.

https://www.eventbrite.co.uk/e/webinar-exploring-the-brain-of-a-fly-registration-43694256698

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Preview of the VFB 2.0 stack browser

VFB 2.0 Stack Browser

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Finding similar neurons using NBLAST

You can now use NBLAST to find similar neurons, or GAL4 drivers that label a neuron of interest. The implementation is described here, and the how, with video demos here. You can start NBLASTing right away on the online app!

Neurons listed in the NBLAST results are linked to VFB, so you can see them on the viewer, together with any other image.

And see here how to find GAL4 drivers that label specific neurons.

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by | February 2, 2016 · 11:56 am

Flybase and Ontology Update

We have just updated to the latest release of the flybase database FB2015_05 and also have updated to the latest (2015-09-16) anatomy ontology.

Please follow the links for further details.

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Feeling adventurous?

Try out our new site which is currently undergoing beta testing:

bit.ly/vfbbeta

We would love to know what you think?

Simply leave a comment here, or use the report an issue or email us links on the site itself.

Expression_download

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by | October 2, 2015 · 11:27 am

Something we’re working on with geppetto.org for next year

geppettoengine:

Data from http://virtualflybrain.org

Something we’re working on with geppettoengine for next year.

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Filed under New Feature, Website

Flybase and Ontology Update

We have just updated to the latest release of the flybase database FB2015_03 and also have updated to the latest (2015-05-12) anatomy ontology.

Please follow the links for further details.

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Now hosting tricolour adult brain stack from Ito 2014

We are proud to announce the addition of a triple stained adult Brain stack to VFB.

Earlier this year, Kei Ito and colleagues on the BrainName consortium published their long awaited new nomenclature for the insect Brain. VFB has followed the evolving BrainName nomenclature since its inception. We are now fully compliant with the published version and have added the gorgeous triple stained half brain shown in this paper to our hosted stacks. (The raw data for this stack is openly available on FlyBase (details and link here).

Ito/BrainName half brain

The detailed, painted mask on this stack includes major tracts such as the great commissure (blue, centre in the above image). We are working on adding a second mask with many more tracts marked. We are also planning to add linked thumbnails from term info to painted domains on both adult brain stacks.

In other news – usage of VFB continues to climb dramatically. We now get over 18,000 hits a month, with all of our many features getting significant usage.

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How do you use VFB?

We’re collecting user stories to assess dev priorities. Please contact us via our blog, or our community group vfb_community@googlegroups.com to let us know.

Feel free to include anything you’d like to use VFB for, not matter how technically difficult it may seem. Please let us know any frustrations you have with current functionality.

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