Category Archives: New Content

New content that is now available

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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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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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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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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Recent development and planned downtime

We have been quiet for a while – this was due to the large volume of new development.

Here are the recent highlights:

  1. Tzumin Lee clone data is now all ready and integrated
  2. FlyCircuit neurons are ready for our 3D stack viewer
  3. Recent version of Chado (07/05/13)has been deployed on the test server and is used for third party stack integration (#1&2)
  4. Updated ontology to comply with the recent Chado

All of the above is now being extensively tested and we expect to see it live shortly.

We plan downtime and partial service disruption next week, that will be required to release recent developments and upgrade storage on the server.

 

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March 19, 2013: Work in progress

We have a few exciting things in the pipeline.

First, we are working on an improved stack viewer, allowing the display of multiple transparent layers. That will be used to display user data with gene expression and anatomy overlays. This viewer is now in alpha-testing.

The new improved stack viewer will allow you to compare expression patterns from Janelia Farm lines and FlyCircuit single neurons, in one stack, at the same time.

These will be coming up shortly, so watch this space!

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