tools

name:opening

**NeuroData Tools** <br>
Joshua T. Vogelstein | 
{[BME](https://www.bme.jhu.edu/),[ICM](https://icm.jhu.edu/),[CIS](http://cis.jhu.edu/),[KNDI](http://kavlijhu.org/)}@[JHU](https://www.jhu.edu/)

.foot[[jovo@jhu.edu](mailto:jovo@jhu.edu) | <http://neurodata.io/talks/> | [@neuro_data](https://twitter.com/neuro_data)]

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### Tools

1. Data Management, Visualization, and Wrangling
  1. [Cloud](https://neurodata.io/ndcloud/)
  2. [ndmg](https://neurodata.io/ndmg) 
  3. [ndreg](https://neurodata.io/ndreg)
2. Statistical Machine Learning
  4. [RerF](https://neurodata.io/rerf/) 
  5. [MGC](https://neurodata.io/mgc/) 
  6. [Graspy](https://neurodata.io/graspy) 
3. Scalable Algorithms
  8. [LOL](https://neurodata.io/lol) 
  7. [clusterNOR](https://github.com/flashxio/knor) 
  9. [FlashX](http://flashx.io/)

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### [Cloud](https://neurodata.io/ndcloud/)

.footnote[[Vogelstein et al. (Nature Methods) 2018](https://www.nature.com/articles/s41592-018-0181-1)]

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### [ndmg](https://neurodata.io/ndmg)

- A Low-Resource Reliable Pipeline to Democratize Multi-Modal Connectome Estimation and Analysis

.footnote[[Kiar et al. (bioRxiv) 2018](https://www.biorxiv.org/content/10.1101/188706v6)]

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#### [ndreg](https://neurodata.io/ndreg)

- Large deformation diffeomorphic metric mapping (LDDMM)
- Fully automatic (no landmarks)
- Modalities: iDisco, CLARITY, MRI, histology, etc.,
- Species: human, rat, mouse, zebrafish...

.footnote[[Kutten et al. (MICCAI) 2016](https://doi.org/10.1007/978-3-319-66182-7_32)]

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### [RerF](https://neurodata.io/rerf)

- generalization of random forests 
- significantly improve over best machine learning algs on >100 benchmark problems

.footnote[[Tomita et al. (arXiv) 2015](https://arxiv.org/abs/1506.03410)]

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### [MGC (pronounced "magic")](https://neurodata.io/mgc)

.footnote[[Vogelstein et al. (eLife) 2019](https://elifesciences.org/articles/41690)]

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### [Graspy](https://neurodata.io/graspy)

.footnote[[Athreya et al. (JMLR) 2018](http://jmlr.org/papers/v18/17-448.html)]

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### [LOL](https://neurodata.io/lol)

.footnote[[Vogelstein et al. (arXiv) 2015](https://arxiv.org/abs/1709.01233)]

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### [clusterNOR](https://github.com/flashxio/knor)

.footnote[[Mhembere et al. (arXiv) 2019](https://arxiv.org/abs/1902.09527)]

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### [FlashX](flashx.io)

.footnote[[Zheng et al. (PPoPP) 2018](https://doi.org/10.1145/3178487.3178501)]

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### References

1. Data Management & Viz: [Vogelstein et al. (Nature Methods) 2018](https://www.nature.com/articles/s41592-018-0181-1)
1. functional & diffusion-MRI: [Kiar et al. (bioRxiv) 2018](https://www.biorxiv.org/content/10.1101/188706v6)
1. Registration: [Kutten et al. (MICCAI) 2016](https://doi.org/10.1007/978-3-319-66182-7_32)
1. Classify/Regress: [Tomita et al. (arXiv) 2015](https://arxiv.org/abs/1506.03410)
1. Hypothesis Testing: [Vogelstein et al. (eLife) 2019](https://elifesciences.org/articles/41690)
1. Graph Stats: [Athreya et al. (JMLR) 2018](http://jmlr.org/papers/v18/17-448.html)
1. Dimension Reduction: [Vogelstein et al. (arXiv) 2015](https://arxiv.org/abs/1709.01233)
1. Clustering: [Mhembere et al. (arXiv) 2019](https://arxiv.org/abs/1902.09527)
1. Scalable Graph/ML Primitives: [Zheng et al. (PPoPP) 2018](https://doi.org/10.1145/3178487.3178501)

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### 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/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/jeremias.png"/>
  <div class="centered">Jeremias Sulam</div>
</div><span style="font-size:200%; color:red;">♥, 🦁, 👪, 🌎, 🌌</span>

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