jefferislab / nblast_clusters_online

Explore clusters from Costa et al. (2014) NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases, online in 3D

NBLAST clusters online

Now live at jefferislab.org/si/nblast/clusters!

This repository contains scripts and supporting files for building interactive webpages showing the clustering of neurons in Costa et al. (2014) NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases.

We have used affinity propagation clustering of our NBLAST scores to cluster the full FlyCircuit dataset of 16,129 neurons into 1,052 distinct clusters of highly related neurons. These clusters have been organised into superclusters, enabling both exploration of the dataset and the matching of individual clusters to morphological types reported in the literature, with these webpages being provided as a tool to enable this exploration. Each supercluster is detailed on its own page, linked to by images on the main page. These pages provide an interactive 3D model of each supercluster with links to pages detailing the clusters contained within. Interactive 3D models of each individual cluster are provided on these pages, as well as information on the constituent neurons and similar clusters as determined by NBLAST.

nblast_clusters_online's Issues

Keep track of recently visited clusters

It would be useful for navigation purposes to display recently visited clusters. Implementation wise, this would probably have to be some JavaScript parsing some kind of cookie.

Add links to VFB from clusters

Could links to VFB viewer be added to the cluster composition table?

http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/clusters/clusters/902/

The top 10 clusters table in nblast on-the-fly links to the clusters online pages, so it would be good to also have links back to VFB from those pages, similar to the ones in nblast on-the-fly results, as it's likely users will navigate clusters that way.

http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/on-the-fly/#query_all=VGlut-F-400093

PNs mixed in with LNs. Why?

Moved from jefferislab/NBLAST_on-the-fly#29.

Separate into VPNs and Central Brain?

Moved from jefferislab/NBLAST_on-the-fly#28.

Add summary labels to superclusters

Moved from jefferislab/NBLAST_on-the-fly#30

Can we use JavaScript to switch neurons on and off in WebGL display?

We could then have a tickbox in the composition table so that users can see only the neurons they want.

Webgl not working on ios8

In chrome, the webgl loads but it's not possible to interact with it. In Safari, the webgl page fails to load.
I've tried other webgl demos with no problem on either browser.

about us should reference cluster version / VFB

Add mention to Neuron paper

Biorxiv one is on title banner.

Add note to mention different between NBLAST and VFB clusters

In response to helpmail from Rachel Wilson in nat-user.

Added to About page.

Loading WebGL is slow

Due to the way the WebGL pages are constructed, the very large WebGL information comes before the rest of the page's HTML, resulting in an almost blank screen while the 3D data is downloaded. It would be better if the 3D data was loaded last, perhaps with a placeholder 'loading...' image, so that the user could look at the rest of the information on the page while waiting.

FlyCircuit links no longer work

Updates to their URLs mean that the neuron links no longer work. C.f. jefferislab/NBLAST_on-the-fly#72

Order individual clusters by similarity

Moved from jefferislab/NBLAST_on-the-fly#31:

http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/clusters/superclusters/11/
i.e. all mAPT etc neurons should co-cluster