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<!DOCTYPE html>
<html>
<head>
<title>NeuroNex:SFN</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
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<textarea id="source">
name:opening
### NeuroData:<br>A community-developed open-source computational ecosystem for big neuro data
Joshua T. Vogelstein
<img src="images/neurodata_blue.png" style="height:150px;float:right;"/>
<br><br><br><br><br>
<img src="images/funding/jhu_bme_blue.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/KNDI.png" STYLE="HEIGHT:95px;"/>
.foot[[jovo@jhu.edu](mailto:[email protected]) | <http://neurodata.io/talks/> | [@neuro_data](https://twitter.com/neuro_data)]
---
### Origin: Hosting public data (2011-)
<img src="images/website_datapage.png" style="width: 100%;"/>
.footnote[<http://neurodata.io/data/>]
---
### ... but, it's hard.
Don’t work alone!
- We set out to revolutionize data management
- And we have had mixed results...
- ...but excited to have seeded a second generation
---
### New Role: A community-developed...
Shift from "build your own" to "see what's available; supplement where necessary."
- Collaborative: across organizations (JHU, Allen, Janelia, Google)
- Cloud computing ecosystem
- End-to-end: data management from microscope to publication
- Spanning paradigms and modalities (EM, AT, MRI, Light Sheet)
- Visualize data at all stages
- Reproducible, extensible analysis ([Jupyter](http://jupyter.org/), [Gigantum](https://gigantum.com/))
---
### What is our software stack?
<img src="images/nd_stack.png" STYLE="height:450px;"/>
.footnote[https://neurodata.io/help/overview/]
---
### Spatial Database: BossDB
- Ported to AWS for scalability
- Random access to arbitrary cutouts
- Downsamples
- Experimental metadata storage (e.g. JSON)
- Authentication
- Spatial queries on annotations
<img src="images/bossDB.png" STYLE="width:100%;"/>
.footnote[https://github.com/neurodata/boss]
---
### NDeX: data to/from cloud
- images: uint8 and uint16
- annotations: uint64
- file formats: png, tiff, jpg, numpy, etc.
- z-slice: flexible naming conventions
- multi-channel
- pip installable
.footnote[https://github.com/neurodata/ndex]
---
### NeuroGlancer for Visualization
.pull-left[
NeuroData Modifications include:
- Boss support
- Multi-color support
- json backend
- Ontology info
]
.pull-right[
<img src="images/AT_rorb.png" style="width: 120%;"/>
]
.footnote[https://github.com/neurodata/neuroglancer]
---
### NDReg for Light sheet registration
<br>
<img src="images/ndreg.png" style="width: 100%;"/>
- LDDMM
- Fully automatic (no landmarks)
- Modalities: iDisco, CLARITY, MRI, histology, etc.,
- Species: human, rat, mouse, zebrafish...
.footnote[https://github.com/neurodata/ndreg]
---
<img src="images/clarity_cells.png" style="position:absolute; left:0px; top:20px; width: 100%;"/>
<!-- <img src="images/synaptomes_pointmatch.png" style="width:100%;"/> -->
<!-- <img src="images/synaptomes_em_light.png" style="width:100%;"/> -->
---
### Current Data Hosting Strategy
- 200+ teravoxels
- 100+ public & private datasets
- 30+ collaborators
- All 3D+ data (no ephys, etc.)
- Costs us cloud pricing
- Investigating distributed model
- Open/excited to collaborate
.footnote[https://neurodata.io/data]
---
### Statistical Machine Learning
- High-Dimensional (non-Euclidean) and Low-Sample Size Data
- [LOL](https://github.com/neurodata/lol), [LumberJack](https://github.com/neurodata/lumberjack), [MGC](https://github.com/neurodata/mgc), [GrasPy](https://github.com/neurodata/graspy), [knor](https://github.com/neurodata/knorR)...
.center[<img src="images/neurodata_tools.png" style="height: 380px"/>]
.footnote[https://neurodata.io/tools/]
---
### Work In Progress
- [FlyWheel](https://flywheel.io/) for data management
- [CloudVolume](https://github.com/seung-lab/cloud-volume) (from Seung Lab)
- Convolutional Dictionary Learning (with [J Sulam](https://sites.google.com/view/jsulam))
- Neuroglancer support for time-series data
- Something with you?
--
### References
1. Vogelstein et al. *Nature Methods* (2018) [[1]](https://rdcu.be/banSS)
2. Kutten et al. *MICCAI* (2018) [[2]](https://link.springer.com/chapter/10.1007%2F978-3-319-66182-7_32)
---
### Acknowledgements
<div class="small-container">
<img src="faces/cep.png"/>
<div class="centered">Carey Priebe</div>
</div>
<div class="small-container">
<img src="faces/randal.jpg"/>
<div class="centered">Randal Burns</div>
</div>
<div class="small-container">
<img src="faces/mim.jpg"/>
<div class="centered">Michael Miller</div>
</div>
<div class="small-container">
<img src="faces/dtward.jpg"/>
<div class="centered">Daniel Tward</div>
</div>
<div class="small-container">
<img src="faces/ebridge.jpg"/>
<div class="centered">Eric Bridgeford</div>
</div>
<div class="small-container">
<img src="faces/vikram.jpg"/>
<div class="centered">Vikram Chandrashekhar</div>
</div>
<div class="small-container">
<img src="faces/drishti.jpg"/>
<div class="centered">Drishti Mannan</div>
</div>
<div class="small-container">
<img src="faces/jesse.jpg"/>
<div class="centered">Jesse Patsolic</div>
</div>
<div class="small-container">
<img src="faces/falk_ben.jpg"/>
<div class="centered">Benjamin Falk</div>
</div>
<div class="small-container">
<img src="faces/kwame.jpg"/>
<div class="centered">Kwame Kutten</div>
</div>
<div class="small-container">
<img src="faces/perlman.jpg"/>
<div class="centered">Eric Perlman</div>
</div>
<div class="small-container">
<img src="faces/loftus.jpg"/>
<div class="centered">Alex Loftus</div>
</div>
<div class="small-container">
<img src="faces/bcaffo.jpg"/>
<div class="centered">Brian Caffo</div>
</div>
<div class="small-container">
<img src="faces/minh.jpg"/>
<div class="centered">Minh Tang</div>
</div>
<div class="small-container">
<img src="faces/avanti.jpg"/>
<div class="centered">Avanti Athreya</div>
</div>
<div class="small-container">
<img src="faces/vince.jpg"/>
<div class="centered">Vince Lyzinski</div>
</div>
<div class="small-container">
<img src="faces/dpmcsuss.jpg"/>
<div class="centered">Daniel Sussman</div>
</div>
<div class="small-container">
<img src="faces/youngser.jpg"/>
<div class="centered">Youngser Park</div>
</div>
<div class="small-container">
<img src="faces/cshen.jpg"/>
<div class="centered">Cencheng Shen</div>
</div>
<div class="small-container">
<img src="faces/shangsi.jpg"/>
<div class="centered">Shangsi Wang</div>
</div>
<div class="small-container">
<img src="faces/tyler.jpg"/>
<div class="centered">Tyler Tomita</div>
</div>
<div class="small-container">
<img src="faces/james.jpg"/>
<div class="centered">James Brown</div>
</div>
<div class="small-container">
<img src="faces/disa.jpg"/>
<div class="centered">Disa Mhembere</div>
</div>
<div class="small-container">
<img src="faces/pedigo.jpg"/>
<div class="centered">Ben Pedigo</div>
</div>
<div class="small-container">
<img src="faces/jaewon.jpg"/>
<div class="centered">Jaewon Chung</div>
</div>
<div class="small-container">
<img src="faces/gkiar.jpg"/>
<div class="centered">Greg Kiar</div>
</div>
<div class="small-container">
<img src="faces/jeremias.png"/>
<div class="centered">Jeremias Sulam</div>
</div><span style="font-size:200%; color:red;">♥, 🦁, 👪, 🌎, 🌌</span>
<img src="images/funding/nsf_fpo.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/nih_fpo.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/darpa_fpo.png" STYLE=" HEIGHT:95px;"/>
<img src="images/funding/iarpa_fpo.jpg" STYLE="HEIGHT:95px;"/>
<img src="images/funding/KAVLI.jpg" STYLE="HEIGHT:95px;"/>
<img src="images/funding/schmidt.jpg" STYLE="HEIGHT:95px;"/>
---
class:center
<img src="images/lion_cartoon2.jpg" style="position:absolute; top:0px; left:0px; height:100%;"/>
</textarea>
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