Category Archives: Usage Examples

Examples of how to use features of the service

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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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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New clusters and display of image stacks

We are pleased to announce a new release of VFB (2013/06/11) including the addition of important new features and content.

New content:

We have integrated lineage clone data from Tzumin Lee’s lab (HHMI-JFRC) (95 clones) [1] and added two new queries: one retrieves lineage clones that overlap a neuropil domain, and the other returns all neurons that are part of a specific lineage. In addition, we have released an improved version of the FlyCircuit neuron clusters obtained by nblast, these clusters now include less outlier neurons than previously. Searches on the site only return results from the current version. If you have done extensive work with the previous clusters, please see our previous post here regarding access to the old version. We also now display the shorter FlyCircuit neuron name (eg. fru-M-000134 instead of  FruMARCM-M001976_seg001) for neurons on the site and for neurons in cluster pages. This is to match the names shown on the FlyCircuit website. We will soon be providing a file with mappings between the long names and short names.

We have also updated the FlyBase Chado and anatomy ontology to the lastest versions, which means more expression results and anatomy information.

New features:

You can now view registered, third party, 3D image data directly on our stack browser in combination with painted neuropil domains. This is true for all registered anatomical dataset currently integrated by VFB: FlyCircuit single neurons (16132 stacks) and the lineage clone data from Tzumin Lee. To display a stack in the viewer, look for the “See in Viewer” link from the term info window or result lists.

We are currently working on being able to display more than one image stack at the same time, and making more image data available in the stack browser including GAL4 lines from Janelia Farm and lineage clones from Kei Ito’s lab (Tokyo University) [2], so keep an eye out for more news.

[1] Yu et al., 2013
[2] Ito et al., 2013

 

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Improved version of neuron clusters

We will be releasing an improved version of the FlyCircuit neuron clusters in the next couple of weeks. Adjusting the clustering method parameters has resulted in an increase in the number of clusters, from 603 to 1062. This means that the neurons in the new clusters are more similar to each other than in the previous version, and the clusters have less outlier neurons.

Once the new cluster version is live on VFB, you’ll still be able to view the old clusters using the URL pattern: http://flybrain.mrc-lmb.cam.ac.uk/vfb/fc/clusters/<exemplar name> (example here), but they will not be searchable on the site. If you have done extensive work on your favourite clusters using the current version and would like to know to which of the new clusters they might correspond to, please get in touch with us (support AT virtualflybrain.org). We would also be able to run and send you the results of queries for clusters that overlap specified brain neuropils using the previous clustering, if you need that.

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Release 28/01/13: Faster queries now live

Our website is now running queries using the superfast ELK reasoner, which means it takes under a second to generate results, even when several queries are run concurrently in different tabs. For more technical details see our previous post.

Together with this latest improvement, today’s release improves the functionality for tracts, displaying a specific query menu for these. You can now search for neuron classes that fasciculate with a tract, for expression (transgene or gene) or for phenotypes that affect a specific tract.

Our users may have experienced intermittent downtime that was required to push the new version live. The service is now fully restored.

 

 

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