Stephen Plaza

Software engineer, researcher, manager in data science, neuroscience, and machine learning

[Stephen Plaza @stephenplaza]

Proud to introduce @janeliaflyem "hemibrain" #hemibrain: a connectome of the Drosophila central brain. https://t.co/MPzPfzTqGj. @stardazed0 @michalj

Please see overview website: https://t.co/i3kJCo34TD

Play with data on neuPrint:
https://t.co/s9X5H84B6f

[Stephen Plaza @stephenplaza]

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[Stephen Plaza @stephenplaza]

We are experimenting with new ways to make EM data like the #hemibrain accessible for data discovery to complement neuPrint. https://t.co/dkxCEE2FZD (with neuroglancer) contains an image search app, an atlas of interesting EM phenomenon, and some annotation tools @janeliaflyem.

[Stephen Plaza @stephenplaza]

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

[Stephen Plaza @stephenplaza]

neuPrint+ is compatible with neuPrint but extends the data model for exploring both inter and intra-cellular interactions. See https://t.co/lkcVqjvWgd for the documented data model additions. We added some support for mitochondria data analysis in the web app and python API.

[Stephen Plaza @stephenplaza]

happy to announce v1.2 release of the #hemibrain before the new year .. now with mitochondria predictions (around 6 million!) and available through "neuPrint+" https://t.co/s9X5H84B6f. @janeliaflyem @stardazed0 https://t.co/GlPIr5JlaN

[Stephen Plaza @stephenplaza]

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.

[Stephen Plaza @stephenplaza]

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

[Greg Jefferis @gsxej]

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 https://t.co/z2nvoLP7Uv. Thanks again to @janeliaflyem @stephenplaza for the transformative #hemibrain #connectomics dataset!

[Stephen Plaza @stephenplaza]

@p2jones @BrainsExplained @liamjdrew https://t.co/p6eHqU5Hxz

[Stephen Plaza @stephenplaza]

@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

[Stephen Plaza @stephenplaza]

@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.

[Stephen Plaza @stephenplaza]

@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

[Stephen Plaza @stephenplaza]

Join @janeliaflyem for a live #hemibrain public discussion on zoom today in a couple hours 11AM-1PM EST (https://t.co/DfWw4LK3av). Lots of interesting topics (geared toward data users) plus a preview of some new results!

[Stephen Plaza @stephenplaza]

@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.

[Stephen Plaza @stephenplaza]

@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

[Stephen Plaza @stephenplaza]

@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

[Stephen Plaza @stephenplaza]

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.

[Stephen Plaza @stephenplaza]

@dachte Fantastic. Look forward to seeing you both!