Stephen Plaza

Proud to introduce @janeliaflyem "hemibrain" #hemibrain: a connectome of the Drosophila central brain. biorxiv.org/content/10.110…. @stardazed0 @michalj Please see overview website: janelia.org/project-team/f… Play with data on neuPrint: neuprint.janelia.org

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Add point or line annotations to the dataset. For the hemibrain, you can perform segmentation mergers to further trace out neurons. These edits are private to the user but we have a 'pull request' feature to submit merge edits for us to incorporate in our next hemibrain release

We are experimenting with new ways to make EM data like the #hemibrain accessible for data discovery to complement neuPrint. clio.janelia.org (with neuroglancer) contains an image search app, an atlas of interesting EM phenomenon, and some annotation tools @janeliaflyem.

neuPrint+ is compatible with neuPrint but extends the data model for exploring both inter and intra-cellular interactions. See neuprint.janelia.org for the documented data model additions. We added some support for mitochondria data analysis in the web app and python API.

We aim to submit a paper in the next month analyzing the mitochondria in the hemibrain. This will provide more information about how to consume this data.

happy to announce v1.2 release of the #hemibrain before the new year .. now with mitochondria predictions (around 6 million!) and available through "neuPrint+" neuprint.janelia.org. @janeliaflyem @stardazed0 youtu.be/RrKQ14pOqm4

@janeliaflyem and @garybhuang paper introducing an unsupervised deep learning strategy to explore large EM volmes (arxiv.org/abs/2012.12175). Potential applications: clustering, object classification, and image search. Initial public version of image search for #hemibrain soon

Read the complete tweeprint describing a full olfactory connectome by starting from the end! Preprint now updated with links to all SI data and code biorxiv.org/content/10.110…. Thanks again to @janeliaflyem @stephenplaza for the transformative #hemibrain #connectomics dataset!

@p2jones @BrainsExplained @liamjdrew elifesciences.org/articles/57443

@BrainsExplained @liamjdrew @stephenplaza Got a link to the paper?

In the fly brain (data from @stephenplaza et al), I was surprised that any 2 totally random neurons are only separated by ~3 connecting interneurons. Challenges the view that the brain is a bunch of separate modules or distinct pathways.

@NeuroSeq @ScottishWaddell @gsxej @janeliaflyem It is possible to proofread and fix small errors locally (such as improving completion of a pathway by a few percent) but we don't have a public platform for this. We might at some point but it is mostly diminished returns to fix these issues manually

@NeuroSeq @ScottishWaddell @gsxej @janeliaflyem The dataset is public but it has been automatically reconstructed and manually proofread to a level that makes something like eyewire mostly unnecessary. If a large error is found, @janeliaflyem will fix it for other groups.

@ScottishWaddell @gsxej @janeliaflyem ls fly Hemi brain connectome open for the public to map neural connections like EyeWire. I am teaching a neuroscience course this fall and plan to have some connectomics lab work. It will make a great lab at the resource-limited institute

@melnattur @denertek @janeliaflyem We were getting a lot of spammers so we closed in new attendees. We might try to do a very formal, private link next time

@stephenplaza @denertek @janeliaflyem That would be good. Tried to join but the host didn't let me in!

Join @janeliaflyem for a live #hemibrain public discussion on zoom today in a couple hours 11AM-1PM EST (hhmi.zoom.us/j/94083683709). Lots of interesting topics (geared toward data users) plus a preview of some new results!

@denertek @janeliaflyem This is meant to be more interactive with Q and A so I wasn't planning to record. We might hold future sessions if there is interest.

@stephenplaza @janeliaflyem any chance this will be recorded and made available?

@real22co @HHMINEWS Sorry, I actually just noticed this question. @philiphubbard is the creator of this visualization and can answer details. He used a combination of surface meshes we create for each neuron and some customized scripts and techniques that leveraged blender I believe

@HHMINEWS if I may inquire...what software was used to create this stunning visual? Incredible work!youtu.be/PeyHKdmBpqY

@dsitaraman Thanks for the suggestions, great points. FWIW, Rubin and Jayaraman labs will be releasing papers on mushroom body and central complex circuitry that heavily uses #hemibrain. Will also be great to hear from people in the community attending to get their experiences

@stephenplaza 2/2: I would also like to know if there are ideas to use this in lab classes from an educational perspective. This is an amazing data set and neuroscience education needs to focus on working with this type of data and approaches.

FlyEM @janeliaflyem is hosting a live public discussion on the #hemibrain and our latest release this June 30th 11AM-1PM ET (zoom link TBA here on the day). Please come with questions/comments. No formal agenda but we can discuss different parts of the data and future plans.

@dachte Fantastic. Look forward to seeing you both!

@stephenplaza I will likely attend with my intern, to help her get a feel for how Janelia does things and how our efforts at Flatiron compare.