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BME.html
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<!DOCTYPE html>
<html>
<head>
<title>Title</title>
<meta charset="utf-8">
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class: center, middle, inverse
# NeuroData:
# Enabling Petascale Neuroscience
### Joshua T. Vogelstein
### {[BME](http://bme.jhu.edu),[ICM](http://icm.jhu.edu),[CIS](http://cis.jhu.edu),[Kavli](http://kndi.jhu.edu)}@[jhu.edu](http://jhu.edu)
#### e: [[email protected]](mailto:[email protected]) | w: [neurodata.io](http://neurodata.io)
---
### Please consider the following _Gedankenexperiment_
#### Experiment 1: collect 10 images in a stack → find all ~100 synapses
1. Look: Open in ImageJ on local computer
2. Pre-process: Manually align images & adjust contrast
3. Annotate: Manually label each synapse
4. Analyze: Plot them all in a 3D scatter plot
---
### Please consider another _Gedankenexperiment_
#### Experiment 2: collect 10K images in a stack → find all 10M synapses
1. Look: Data too large to load into ImageJ on local computer
2. Pre-process: Takes too long to manually pre-process
3. Annotate: Takes even longer find find all synapses
4. Analyze: Can't really see what is going on when plotting 10M synapses
---
### Oppurtunity: Datasets like this are popping up all over the place
<!-- # Case Study -->
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- Real Experiment: Serial Electron Microscopy
- Resolution: 4 x 4 x 40 nm^3
- Volume: 350 x 450 x 50 micron^3
- Size: ~10 TB
Note: the above video is from Kasthuri et al. (Cell, 2015), but the data we are discussing are from Bock et al. (Nature, 2011)
---
.pull-left[
### Challenge: Can't perform any of the 4 steps to discovery
<br></br>
#### 4 Steps to Discovery:
1. Look
1. Pre-Process
1. Annotate
1. Analyze
]
.pull-right[
### Action: Meet needs to achieve each step
<br></br>
#### 3 Needs to Achieve:
<ol type="A">
<li>Algorithms</li>
<li>Software</li>
<li>Computer</li>
</ol>
]
---
# Resolution: NeuroData!
### We make the following open science contributions to the community:
- reference datasets in a variety of modalities
- reference pipelines for operating on such data
- Web-services to enable using our data-intensive computing
- A cloud computing stack to facilitate analysis
- Detailed specs for plugging in different routines
- Data derivatives at all stages of analysis
### It is now easier to:
- Bridge across scales and modalities
- Answer questions the require scale
- Engage complementary expertise
- Reproduce results
---
# What this talk is about
<br></br>
- A case study
- For each step, we explain the needs
- For each need, we explain why the classic approach fails
- We then provide our approach to filling those needs
---
# Case Study
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- Experiment: Serial Electron Microscopy
- Resolution: 4 x 4 x 40 nm^3
- Volume: 350 x 450 x 50 micron^3
- Size: ~10 TB
- Question: Are synapses distributed uniformly in space?
---
# 3 Needs to Achieve
.pull-left[
### 1. Computer
<ol type="i">
<li>Data-Intensive Cluster</li>
<li>High-Performance Cluster</li>
<li>Local Thin Client</li>
</ol>
]
.pull-left[
### 2. Software
<ol type="i">
<li>Spatial database</li>
<li>Annotation database</li>
<li>Data Exchange</li>
<li>Distributed Analytics Stack</li>
</ol>
]
.pull-left[
### 3. Algorithms
<ol type="i">
<li>Volume reconstruct</li>
<li>Histogram normalize</li>
<li>(register to atlas)</li>
<li>Synapse detection</li>
<li>Spatial statistics</li>
</ol>
]
.footnote[
### Note: each step to discovery has different specs with respect to each of these.
]
---
# Need #1: Computers
<br></br>
| | _Sub-Need_ | | _Reason_ | _Example_ |
| --- | :--- | --- | :---- | :--- |
| 1 | Data intensive | | Store TBs | DataScope |
| 2 | High-Performance | | Process TBs | MARCC |
| 3 | Local Thin Client | | Control them | MacBook Air |
<div style="width: 480px; height: 360px; margin: 10px; position: relative;"><iframe allowfullscreen frameborder="0" style="width:480px; height:360px" src="https://www.lucidchart.com/documents/embeddedchart/d8725eac-b41f-403b-8820-f189483d33b0" id="uMmrHtqX_k1u"></iframe></div>
---
# Need #2: Software
<br></br>
| | _Sub-Need_ | | _Reason_ | _Runs On_ |
| --- | :--- | --- | :---- | :--- |
| 1 | Spatial Database | | fast IOPS | Data Intensive |
| 2 | Annotation Database | | fast FLOPS | HPC |
| 2 | Distributed Analytics Stack | | fast FLOPS | HPC |
| 3 | Terminal/Web-Browser | | Control them | Thin Client |
<div style="width: 480px; height: 360px; margin: 10px; position: relative;"><iframe allowfullscreen frameborder="0" style="width:480px; height:360px" src="https://www.lucidchart.com/documents/embeddedchart/d8725eac-b41f-403b-8820-f189483d33b0" id="uMmrHtqX_k1u"></iframe></div>
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