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<!DOCTYPE html>
<html>
<head>
<title>Neuronex19</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
<link rel="stylesheet" href="fonts/quadon/quadon.css">
<link rel="stylesheet" href="fonts/gentona/gentona.css">
<link rel="stylesheet" href="slides_style.css">
<script type="text/javascript" src="assets/plotly/plotly-latest.min.js"></script>
</head>
<body>
<textarea id="source">
name:opening
#### Ailey in an Hour:<br>(A "Soup-to-Nuts" Pipeline for Analysis of Whole Cleared Brain Data)
<!-- {[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/) -->
<a href="https://neurodata.io"><img src="images/neurodata_purple.png" style="height:390px;"/></a>
<!-- <img src="images/funding/jhu_bme_blue.png" STYLE="HEIGHT:95px;"/> -->
<!-- <img src="images/funding/KNDI.png" STYLE="HEIGHT:95px;"/> -->
<!-- <font color="grey"></font> -->
.foot[[Joshua T. Vogelstein](https://neurodata.io) | [jovo@jhu.edu](mailto:[email protected]) | [neurodata.io](http://neurodata.io) | [@neuro_data](https://twitter.com/neuro_data)]
---
<img src="faces/baby_violette.jpg" style="position:absolute; top:0px; left:0px; height:100%;"/>
---
### [Reggie](https://neurodata.io/reg/)
Pipeline for analysis of CLARITY/COLM/iDisco/etc. data
- Downloads 2D tiles from cloud
- Cleans artifacts
- Stitch 2D tiles into 3D volume using Terastitcher
- Downsample to atlas resolution
- Nonlinear registration atlas to data
- Inverts registration to atlas
- Upsample registration to native resolution
- .gold[Detect all cells (works ok)]
- .r[Track all processes (nothing works yet out of the box for us)]
- Upload registered brain and atlas to cloud
- Visualize registered brain in cloud
- Democratize access
---
### [Reggie](https://neurodata.io/reg/)
<img src="images/reggie.png" style="width:100%;"/>
- [Open source](https://github.com/neurodata/ardent)
- [Documented with tutorials](https://ardent.neurodata.io/demo/demo.html)
- [pip installable](https://ardent.neurodata.io/install.html)
- GPU and distributed support
- Mostly automatic
- .r[Runs in a 1 hour] on LaVision data
- .r[Runs in a 9 hours] on 1 TB data (COLM)
---
### LaVision → Overlay ← Allen Atlas
<a href="https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=grp62z6p_By_7Q">
<img src="images/lavision_mouse.png" style="position:absolute; left:0px; width:100%;"/>
</a>
.footnote[ (from Ailey Crow at Karl Deisseroth)]
---
### Rat COLM → Overlay ← Waxholm
<a href="https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=Zylae4o-KUXayQ">
<img src="images/colm_mouse.png" style="position:absolute; left:0px; width:100%;"/>
</a>
.footnote[ (1 TB image from Ailey Crow at Karl Deisseroth)]
---
### LaVision iDisco Rat ← Waxholm Atlas
<a href="https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=LIky0E7KVaEaBg">
<img src="images/idisco_rat.png" style="position:absolute; left:0px; width:100%;"/>
</a>
.footnote[ .w[(from Audrey Branch at Michela Gallagher)]]
---
### Human MRI → Overlay ← Desikan
<a href="https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=1W2-JxfOQIvLqA">
<img src="images/mri_human.png" style="position:absolute; left:0px; width:100%;"/>
</a>
<!-- .footnote[ (?)] -->
---
.headnote[Allen Atlas + CLARITY + AI Cell Detection (from Ailey Crow at Karl Deisseroth)]
<a href="https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=nXUxo32Juxit-A">
<img src="images/neuroglancer_ara.png" style="position:absolute; left:0px; top:60px; width:100%;"/>
</a>
---
### Data Visualization & Democratization
- From local to web viz with atlas overlays ([Neuroglancer](https://github.com/google/neuroglancer))
- From spatial database to flat files ([zarr](https://zarr.readthedocs.io/en/stable/)+[n5](https://github.com/saalfeldlab/n5) coming soon)
- From centralized to distributed storage (no more [BOSS](https://github.com/jhuapl-boss/boss))
- From blosc to brotli compression ([brotli](https://github.com/google/brotli))
---
### Discussion
- LDDMM previously implemented in [ITK](https://github.com/InsightSoftwareConsortium/ITKNDReg/), but lacked GPU support
- Nonlinear registration works well across modalities and taxa
- Integrating 2D to 3D ([paper here](https://link.springer.com/chapter/10.1007/978-3-030-33226-6_18))
- Integrating missing data and artifacts [paper here](https://doi.org/10.1101/494005)
- Applying now to Janelia [MouseLight](https://www.janelia.org/project-team/mouselight) project
- Working on BICCN with Brain Architecture and Pavel Osten
- Working with Sam Wang to integrate atlas with full cerebellum
- Integrating into [scikit-image](https://scikit-image.org) (widely used image library)
- Active development, community participation encouraged!
--
#### Lessons learned
- New cloud technology enables more scalable data access
- From developer to integrator
- Open-source, community-developed, widely-used, general tools
- Highly collaborative: Google, Janelia, CSHL, APL, Stanford, JHU...
---
### Papers
- A. Charles, et al. [Towards Community-Driven Big Open Brain Science](mailto:[email protected]). Annual Reviews in Neuroscience, 2020.
- J. T. Vogelstein, et al. [A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data](https://www.nature.com/articles/s41592-018-0181-1). Nature Methods, 2018.
- A. Branch, et al. [An optimized protocol for iDISCO+ rat brain clearing, imaging, and analysis](https://doi.org/10.1101/639674). bioRxiv, 2019.
- D. J. Tward, et al. [Diffeomorphic registration with intensity transformation and missing data: Application to 3D digital pathology of Alzheimer's disease](https://doi.org/10.1101/494005). bioRxiv, 2019.
- D. J. Tward, et al. [3D Mapping of Serial Histology Sections with Anomalies Using a Novel Robust Deformable Registration Algorithm](https://link.springer.com/chapter/10.1007/978-3-030-33226-6_18). International Workshop on Multimodal Brain Image Analysis, 2019
- V. Chandrashekhar, Nonlinear Registration for all. In prep.
---
### Code
- [NeuroData Cloud](http://neurodata.io/nd_cloud)
- [Reggie](https://neurodata.io/reg/)
- [Neuroglancer visualization](https://github.com/google/neuroglancer) (not us)
- [Zarr file format](https://zarr.readthedocs.io/en/stable/) (not us)
- [n5](https://github.com/saalfeldlab/n5) (not us)
- [Brotli compression](https://github.com/google/brotli) (not us)
- [Scikit-Image](https://scikit-image.org) (not us)
---
### Website: [neurodata](https://neurodata.io)
<img src="images/google_analytics.png" style="width:60%;"/>
- $\approx$ 100,000 unique visitors to date
- $>$130 countries & $>$3,000 cities
- $>$5,600 twitter followers
- Support data from $>$30 labs (including several NeuroNex PIs)
- Modalities/scales: EM/nano, LM/micro, MRI/milli
- Taxa: worms, flies, fish, mice, rats, sea lions, coyotes, non-human primates, humans
---
### Acknowledgements
<!-- <div class="small-container">
<img src="faces/ebridge.jpg"/>
<div class="centered">Eric Bridgeford</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/yummy.jpg"/>
<div class="centered">yummy</div>
</div>
<div class="small-container">
<img src="faces/lion_skateboard.jpg"/>
<div class="centered">lion</div>
</div>
<div class="small-container">
<img src="faces/violet.jpg"/>
<div class="centered">baby girl</div>
</div>
<div class="small-container">
<img src="faces/jklv.jpg"/>
<div class="centered">family</div>
</div>
<div class="small-container">
<img src="faces/earth.jpg"/>
<div class="centered">earth</div>
</div>
<div class="small-container">
<img src="faces/milkyway.jpg"/>
<div class="centered">milkyway</div>
</div>
<br>
<!-- -- -->
<!-- <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/cshen.jpg"/>
<div class="centered">Cencheng Shen</div>
</div> -->
<!-- <div class="small-container">
<img src="faces/bruce_rosen.jpg"/>
<div class="centered">Bruce Rosen</div>
</div> -->
<!-- <div class="small-container">
<img src="faces/kent.jpg"/>
<div class="centered">Kent Kiehl</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/vikram.jpg"/>
<div class="centered">Vikram Chandrashekhar</div>
</div>
<!-- <div class="small-container">
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<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/devin.jpg"/>
<div class="centered">Devin Crowley</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/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/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> -->
<!--
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<div class="centered">Meghana Madhya</div>
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<!-- <div class="small-container">
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<div class="centered">Percy Li</div>
</div>
-->
<!-- <div class="small-container">
<img src="faces/hayden.png"/>
<div class="centered">Hayden Helm</div>
</div> -->
<!-- <div class="small-container">
<img src="faces/satish.png"/>
<div class="centered">Satish Palaniappan</div>
</div> -->
<!-- <div class="small-container">
<img src="faces/nate.png"/>
<div class="centered">Nate Anderson</div>
</div> -->
<!--
<div class="small-container">
<img src="faces/fan.png"/>
<div class="centered">Qiuyun Fan</div>
</div> -->
<br>
</div>
<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;"/> -->
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---
class:center
<img src="faces/lion_swing.jpg" style="position:absolute; top:0px; left:0px; height:100%;"/>
.headnote[Questions?]
---
class: middle, inverse
## .center[Extra Slides]
---
<a href="https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=LdxWc0NSQTZhXg">
<img src="images/precomputed_brotli.png" style="position:absolute; left:0px; width:100%;"/>
</a>
.footnote[Precomputed + Brotli + EM (from [Forrest Collman](https://alleninstitute.org/what-we-do/brain-science/about/team/staff-profiles/forrest-collman/) at Allen Institute)]
---
### Centralized vs. Distributed
| Property | Centralized | Distributed
|:--- |:--- |:--- |
| Developer | Us → APL | Community
| Where are data | cloud | cloud
| Access rates | ~100 mbps | ~100 mbps
| Who pays | me | you
| Who is in control | me | you
| Who has access | up to me | up to you
| Costs | more | less
| Who manages | all me | me + you + new software
| Our current | yes | yes
| Our plan | no | yes
---
### File Formats
| Property | [BOSS](https://github.com/jhuapl-boss/boss) | CloudVolume + [Precomputed](https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed) | [Zarr](https://zarr.readthedocs.io/en/stable/) + [n5](https://github.com/saalfeldlab/n5)
|:--- |:--- |:--- |
| Developer | Us → [Will Gray Roncal](https://bossdb.org/about) | [Seung Lab](http://seunglab.org/) + [Google](https://github.com/google/neuroglancer/graphs/contributors) | [Biologists](https://www.cggh.org/) + [Saalfeld Lab](https://www.janelia.org/lab/saalfeld-lab)
| Last commit | Aug 9 | Sep 26 | yesterday
| Used by (github) | 0 | 18 | 121
| User Auth | yes | no | no
| Data Management | yes | no | no
| Our current | most | some | none
| Our plan | no | maybe | probably
---
### Compression
| Property | [Blosc](http://blosc.org/) | [Gzip](https://www.gzip.org) | [Brotli](https://github.com/google/brotli)
|:--- |:--- |:--- |
| Developer | [some guy](http://blosc.org/pages/francesc-alted-resume/)| [GNU](https://www.gnu.org/home.en.html) | [Google]()
| Lat commit | Sep 30 | 2018 | Oct 2
| Used by (github) | ? | $\gg 0$ | 502
| Browser support | none | all | all
| Compression size | ok | good | better
| Decompression speed | great | good | good
| Compression speed | great | good | ok
| Our current | most | some | none
| Our plan | none | none | all
---
### Visualization
| Property | [Fiji/ImageJ](https://imagej.net/Fiji) | [CATMAID](https://catmaid.readthedocs.io/en/stable/) | [Neuroglancer](https://github.com/google/neuroglancer)
|:--- |:--- |:--- |
| Developer | [scientists](https://github.com/imagej/imagej/graphs/contributors)| [Janelia](https://github.com/catmaid/CATMAID/graphs/contributors) | [Google](https://github.com/google/neuroglancer/graphs/contributors)+us
| Lat commit | Oct 8 | yesterday | yesterday
| Used by (github) | ? | ? | 18
| Web | no | yes | yes
| skeletons | yes | yes | yes
| volume annotations | yes | recently | yes
| analysis | lots | skeletons | none
| atlas overlay | yes | maybe | yes
| Our current | local | none | all
| Our plan | local | none | all
---
### Registration
| Property | [Reggie](https://neurodata.io/reg/) | [NDReg](https://github.com/InsightSoftwareConsortium/ITKNDReg) | [ANTS](https://github.com/ANTsX/ANTs) | [skimage](https://scikit-image.org)
|:--- |:--- |:--- |
| Developer | [Us](https://github.com/neurodata/ardent/graphs/contributors)| [ITK](https://github.com/InsightSoftwareConsortium/ITKNDReg/graphs/contributors) | [Brian Avants](http://stnava.github.io/) | [300+](https://github.com/scikit-image/scikit-image/graphs/contributors)
| Lat commit | yesterday | Aug 21 | yesterday | yesterday
| Used by | just us | nobody? | MRI people | millions?
| Used by (github) | 0 | 0 | ? | 26,500
| Linear registration | yes | yes | yes | no
| LDDMM | yes | yes | approximate | no
| GPU Support | yes | no | no | no
| cleared brains | yes | yes | no | no
| Our current | yes | no | no | no
| Our plan | yes | no | no | yes
---
### Access Rates
<img src="images/centralized_vs_distributed.png" style="width:650px;"/>
---
### [Benchmarks](https://www.opencpu.org/posts/brotli-benchmarks/)
<!-- <img src="images/brotli_size.png" style="height:270px;"/>
<img src="images/brotli_compress.png" style="height:270px;"/>
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<div style="display:inline-flex">
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Size
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Decompress
<img src="images/brotli_decompress.png" alt="nah" style="height:380px">
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Compress
<img src="images/brotli_compress.png" alt="nah" style="height:380px">
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brotli = red, gzip = blue
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