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WEBINAR: Exploring the brain of a fly

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.

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Major new VFB release

We are proud to announce a major new VFB release. This sees some very significant enhancements to the data we serve: we have now mapped ~50% of the >16,000 single neurons from FlyCircuit to published neuron classes; we now host almost 18,000 images of VT lines along with curation of where they are expressed.

An example of the detailed image data available for neuron classes can be see by querying for neurons with synaptic terminals in the protocerebral bridge and sorting on available images. 111 of the 137 neuron classes returned are illustrated by one or more single neuron images:

Screen Shot 2016-08-10 at 11.40.18

This particular data comes from combining NBLAST clusters (described in a recent paper from VFB’s Marta Costa and Greg Jefferis) and detailed curation of the paper from Ann-Shyn Chiang’s group ‘A comprehensive wiring diagram of the protocerebral bridge for visual information processing in the Drosophila brain.’

Any of these neuron images can be used to search for predicted GAL4 driver lines using NBLAST on the fly (video tutorial).

We are working on integrating NBLAST queries directly into VFB, so soon you’ll be able obtain lists of predicted driver lines directly from neuron classes.

We now have ~18,000 images of VT expression patterns. Registered data kindly donated by Barry Dickson (Janelia/IMP), Katja Buhler (VRVis) and colleagues was bridged from the original T1 template space to the JFRC2 template used on the VFB site.

The VT lines are indexed to gross neuropils (data from BrainBase), e.g.

Screen Shot 2016-08-10 at 12.02.14

They are also indexed to individual neurons (curated from the literature):

Screen Shot 2016-08-10 at 12.00.54

This release also includes many more minor enhancements and extensions to data via curation by VFB and FlyBase of anatomy, expression and phenotypes.


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VFB 1.5 Launch – Monday 15th Feb

We are delighted to announce the official release of VFB 1.5. This
has already been available in beta for some time. It will become the
official version of VFB on Monday 15th Feb.

The new site features a new look and feel, a much improved image
browser and better integration of images into search results. Please
let us know what you think. Your feedback is essential to our
continued improvement.

The main focus of development is now our new 3D browser (watch this
space for demos) and improvements to our data architecture to speed
up the site, extend queries and support new visualisation tools.

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February 2013 report: work and stats

Last month we focussed on the following:

1. Improving server stability

2. Working on stack registration in order to release image data from the recent Janelia Farm GAL4 line set and FlyCircuit in our 3D image browser. We will announce once these are ready, so watch this space.

3. Extending queryable content on the site to include all stages and regions of the nervous system.

Server statistics:

The VFB site now regularly receives over 1,100 visits a month with these visitors viewing over 4000 pages in total. Top 3 countries for February are:

Country/Territory             Visits
1.    United States            332
2.    United Kingdom       308
3.    Germany                   86

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An update on work in progress

In the past two weeks we have been working on some strategic goals:

1. Experimenting with opening content for more stages

2. Working on aspects of and applying for funding for community annotation for the VFB.

The server uptime was 99.9999% for the past three weeks.

Keep in touch and send us your feedback on

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Improved server stability

We are glad to announce that our efforts on improving server monitoring, aided by an apparently more stable reasoner, have proven fruitful.

Over the past week, total server interruption time was less than a minute, and according to Google tools, the site was accessible 99.99% of time.

We hope you enjoy the more reliable Virtual Fly Brain site and please let us know if you spot anything unusual on


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1000+ Hits a Month!

We are pleased to announce that between 7 Jan and 7 Feb this year the site has been accessed over 1000 times – for the first time since the site’s launch in 2011! The number of pages viewed in that time was over 4000 (up 30% on the previous month).

We thank all our users for their support and use this opportunity to announce some important new development that we are currently working on:

  1. Enabling access to the content for more developmental stages and
  2. Displaying “real-life” 3D stacks for some of our data.

These will be released and announced shortly, so watch this space!


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New faster reasoner in beta-testing

We are pleased to announce that we are moving to the new superfast reasoner ELK for all of our queries. The new reasoner is an order of magnitude faster than the present, JFact based reasoner. With the new reasoner the longest expression queries take just under 1 sec to return.

Those of you geeky enough to be interested in technical details might want to check out Samuel Croset’s Brain library, which we used in the implementation.

The new application is now in beta-testing. Watch this space for the official release announcement



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Continuing intermittent problems on VFB

Unfortunately the problems with our servers are ongoing. That is likely to result in our website going down intermittently. Apologies to all our users, we’re working hard to solve this problem.

We will make an announcement when the problems are resolved.

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VFB is looking for user stories for pending grant applications

If you have a story about some nugget of information you’ve found on VFB that has proven useful to your research, please share it with us – either as a comment on this blog post or via email to support at virtualflybrain dot org.

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