Monthly Archives: May 2013

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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Filed under New Content, New Feature, Usage Examples

IIP3D upgrade – v 1.0.1

We have upgraded the IIP3D server (the software that renders 3D stacks for our viewer) to the most recent version 1.0.1.

This upgrade provides slightly faster rendering, keeps us abreast with the release cycle of the IIP3D software, but most importantly, it provides new features required for for rendering user and third party stacks.

This upgrade is an important stepping stone in preparation for releasing images of clones, neurons and GAL4 lines on our stack browser. The release of the first batch of this image data to our stack browser is now imminent.

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Filed under Site Issues

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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Filed under New Content, Site Issues

New version of IIP3D is in testing

We are currently testing new version of the IIP3D server, the core software used for rendering 3D stacks on our site.

The new features of IIP3D will allow us to deliver third party image stacks to the VFB site users.

Below is an example of the stack from Tzumin Lee’s recent data set (http://www.janelia.org/lab/lee-tzumin-lab):

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