Category Archives: New Feature

New features that are now available

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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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

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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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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New VFB release: queries available for all neuroanatomy terms and Janelia FlyLight 3D images on stack viewer

We are pleased to announce a new release of VFB, including the ability to query the whole adult, larval and embryonic neuroanatomy,  and to layer the Janelia FlyLight 3D images on the stack viewer.

Users can now choose to query  ‘All Neuroanatomy’ or to restrict their queries to ‘Adult Brain’. Queries can now be done on , the adult thoracico-abdominal ganglion, sense organs, and motor neurons, among others. For example, searching for ventral cibarial sense organ:

searching for sense organs

 Find the term on the autocomplete and select it.

cibarial_organ

From here, further queries on expression are possible, just as previously for the adult brain.

cibarial_trangenes

We have also added the ability to layer the 3D Janelia FlyLight images on stack viewer. Users can now build composite images with any of the Janelia lines, FlyCircuit neurons, neuroblast and fruitless clones.

Janelia 3D images can be added from any expression queries, clicking on ‘See in Viewer’.  For example, a query for transgenes expressed in the ‘wedge’ lists:

wedge

Looking at GMR27B03 in the stack viewer:

janelia_stack

You can now build composite images with the Janelia lines. For any image in the stack viewer, click ‘Add to composite view’, and then go back to run more queries and add any other images you want (up to 3 at a time for each composite).

composite

You have any any feedback please let us know!

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New VFB release – extensive lineage clone data and images added; layer multiple 3D images in the stack viewer

We are excited to announce a new release of VFB, featuring a full set of adult central brain lineage clone images and mapping data from Ito et al., 2013 & Yu et al., 2003 + fruitless expressing clones from Cachero and Ostrovsky et al., 2010. The mapping data we’ve added includes mapping to brain regions and mapping of single neurons and fru expressing lineage clones to complete central brain lineage clones. We’ve also added functionality for display of multiple images on our stack browser. In combination with new functionality allowing multiple registered images. The combination of these functionalities provides opportunities for querying and exploring lineage data that are unavailable from any other resource.

To search textually for clones, simply type ‘clone’ into the text search box on the front page or :

clone search

To query by region:

clone query

clone query result

All clones from the Ito and Yu papers and most from Cachero come with linked thumbnail images.

clone thumbs

Any of these thumbnails can be added to the stack browser:

AOTUv4 clone on stack

You can layer up to 3 image stacks in a single browser view:

3 layers on stack

Images that can be added to the stack browser include > 16000 neurons from the FlyCircuit dataset. We plan to add downloads for many of our registered stacks in the near future.

Many thanks to Kei Ito & Tzumin Lee for providing us with data and mapping tables to make this release possible.

We hope you enjoy the new content and features. Please let us know what you think,

The VFB team.

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Overlaying image stacks

We are pleased to announce the addition of a major functionality to the site. It is now possible to overlay image stacks on our Viewer, making it much easier to compare between them. For details on how to create a composite view click here.

Right now, you can compare up to three stacks of any of the FlyCircuit neurons or lineage clones available. Very soon, we will be adding even more registered image data!

 

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Improvements in speed of display

Third-party registered  image stacks, such as the FlyCircuit neurons and lineage clones  now load much quicker on our Viewer. We hope these improvements enable users to look at the registered images, even when using a slower internet connection.

In 2 to 3 weeks, we will be adding even more image stacks to the site, so stay tuned!

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