-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathextra.html
474 lines (353 loc) · 8.88 KB
/
extra.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
<!DOCTYPE html>
<html>
<head>
<title>Title</title>
<meta charset="utf-8">
<style>
@import url(https://fonts.googleapis.com/css?family=Droid+Serif);
@import url(https://fonts.googleapis.com/css?family=Yanone+Kaffeesatz);
@import url(https://fonts.googleapis.com/css?family=Ubuntu+Mono:400,700,400italic);
body {
font-family: 'Droid Serif';
}
h1, h2, h3 {
font-family: 'Yanone Kaffeesatz';
font-weight: 400;
margin-bottom: 0;
}
.remark-slide-content h1 { font-size: 3em; }
.remark-slide-content h2 { font-size: 2em; }
.remark-slide-content h3 { font-size: 1.6em; }
.footnote {
position: absolute;
bottom: 3em;
}
li p { line-height: 1.25em; }
.red { color: #fa0000; }
.large { font-size: 2em; }
a, a > code {
color: rgb(249, 38, 114);
text-decoration: none;
}
code {
background: #e7e8e2;
border-radius: 5px;
}
.remark-code, .remark-inline-code { font-family: 'Ubuntu Mono'; }
.remark-code-line-highlighted { background-color: #373832; }
.pull-left {
float: left;
width: 47%;
}
.pull-left-bottom {
float: left;
width: 47%;
bottom: 0;
}
.pull-right {
float: right;
width: 47%;
}
.pull-right ~ p {
clear: both;
}
#slideshow .slide .content code {
font-size: 0.8em;
}
#slideshow .slide .content pre code {
font-size: 0.9em;
padding: 15px;
}
.inverse {
background: #272822;
color: #777872;
text-shadow: 0 0 20px #333;
}
.inverse h1, .inverse h2 {
color: #f3f3f3;
line-height: 0.8em;
}
/* Slide-specific styling */
#slide-inverse .footnote {
bottom: 12px;
left: 20px;
}
#slide-how .slides {
font-size: 0.9em;
position: absolute;
top: 151px;
right: 140px;
}
#slide-how .slides h3 {
margin-top: 0.2em;
}
#slide-how .slides .first, #slide-how .slides .second {
padding: 1px 20px;
height: 90px;
width: 120px;
-moz-box-shadow: 0 0 10px #777;
-webkit-box-shadow: 0 0 10px #777;
box-shadow: 0 0 10px #777;
}
#slide-how .slides .first {
background: #fff;
position: absolute;
top: 20%;
left: 20%;
z-index: 1;
}
#slide-how .slides .second {
position: relative;
background: #fff;
z-index: 0;
}
/* Two-column layout */
.left-column {
color: #777;
width: 20%;
height: 92%;
float: left;
}
.left-column h2:last-of-type, .left-column h3:last-child {
color: #000;
}
.right-column {
width: 75%;
float: right;
padding-top: 1em;
}
br {
line-height: 50%;
}
</style>
<!-- load remark -->
<script src="http://gnab.github.com/remark/downloads/remark-0.5.1.min.js" type="text/javascript"></script>
<!-- load MathJax -->
<script type="text/javascript"
src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML&delayStartupUntil=configured"></script>
<!-- Initialize (has to go in <script> tag **without** SRC attribute) -->
<script type="text/javascript">
// Create slideshow
var slideshow = remark.create({
// This BREAKS MathJax:
// highlightLanguage: 'Python'
// You have to tag every code block with python, like so:
//
// ```python
// def add(a, b):
// return a + b
// ```
});
// Setup MathJax
MathJax.Hub.Config({
tex2jax: {
skipTags: ['script', 'noscript', 'style', 'textarea', 'pre']
}
});
MathJax.Hub.Queue(function() {
$(MathJax.Hub.getAllJax()).map(function(index, elem) {
return(elem.SourceElement());
}).parent().addClass('has-jax');
});
MathJax.Hub.Configured();
</script>
</head>
<body>
<textarea id="source">
---
.pull-left[
### 4 Steps to Discovery:
1. Look
1. Pre-Process
1. Annotate
1. Analyze
]
---
# Algorithm Needs
### Look
| _Sub-Need_ | | _Reason_ |
| :--- | --- | :---- |
| Tile Cache | | Render and pre-fetch images |
| Web-Viz | | Display images & metadata |
| Extract Surfaces | | Build geometric objects for analysis |
### Image Process
| _Sub-Need_ | | _Reason_ |
| :--- | --- | :---- |
| Volume Reconstruct | | Images are not aligned off scope |
| Histogram Normalize | | Exposure & objective aberrations |
| (Register to Atlas) | | Obtain reference coordinate system |
---
# Algorithm Needs (cont'd)
### Scene Parse
| _Sub-Need_ | | _Reason_ |
| :--- | --- | :---- |
| Label | | Manually label objects of interest |
| Train | | Train machine vision algorithms |
| Test | | Qualitative & quanitative assessment & cross-validation |
| Deploy | | Run at scale |
--
### Analyze
| _Sub-Need_ | | _Reason_ |
| :--- | --- | :---- |
| Query Objects | | Analyze objects of interest |
| Estimate Statistics | | Quantify parameters |
| Model Check | | Cuz all models are wrong |
---
## Answering Scientific Questions from Data
1. Look
1. Pre-Process
1. Annotate
1. Analyze
---
## Answering Scientific Questions from Data
1. Look
1. Pre-Process
1. Annotate
1. Analyze
### What do you need to achieve these things
<br></br>
| | _Need_ | | _Example_ | _Sufficient?_ |
| --- | :---: | --- | :----: | :---: |
| A. | Computer | | Dell Workstation | :) |
| B. | Software | | Local MATLAB | :) |
| C. | Algorithms | | deconvolution | :) |
<!-- | 4 | Data Exchange | | load image, save csv| :) |
-->
---
## Answering Scientific Questions from BIG Data
1. Look
1. Pre-Process
1. Annotate
1. Analyze
---
## Answering Scientific Questions from BIG Data
1. Look
1. Pre-Process
1. Annotate
1. Analyze
### What do you need to achieve these things
<br></br>
| | _Need_ | | _Example_ | _Sufficient?_ |
| --- | :---: | --- | :----: | :---: |
| A. | Computer | | Dell Workstation | :( |
| B. | Software | | Local MATLAB | :( |
| C. | Algorithms | | deconvolution | :( |
<!-- | 4 | Data Exchange | | load image, save csv |:( | -->
<br></br>
I take it as given that everyone here understands *why* we do the first quadruple,
and why we need the next quadruple to make them happen?
---
.pull-left[
### Hardware
- Data-Intensive Cluster
- High-Performance Cluster
- Local Thin Client
]
--
.pull-left[
### Software
- Spatial database
- Annotation database
- LIM system
- Tile cache
- Data exchange
- Web-viz
- Distributed analytics stack
]
--
.pull-left[
### Algorithms
- Volume reconstruct
- Histogram normalize
- (register to atlas)
- Synapse detection
- Spatial statistics
]
---
# 4 Steps to Discovery
.pull-left[
### 1. Look (24 fps)
<ol type="i">
<li>Pan in X, Y, Z</li>
<li>Zoom in & out</li>
<li>Overlay labels</li>
</ol>
]
.pull-left[
### 3. Annotate (< 3 days)
<ol type="i">
<li>Label</li>
<li>Train</li>
<li>Spot check</li>
<li>Hyper-parameter sweep</li>
<li>Assess</li>
<li>Run at scale</li>
</ol>
]
.pull-left[
### 2. Pre-Process (< 1 day)
<ol type="i">
<li>Volume reconstruct</li>
<li>Histogram normalize</li>
<li>(register to atlas)</li>
</ol>
]
.pull-left[
### 4. Analyze (< 1 days)
<ol type="i">
<li>Query synapses</li>
<li>Estimate distribution</li>
<li>Compute p-value</li>
</ol>
]
---
### Big Data Challenges
- hardware infrastructure to support data intensive & high performance computing
- software optimized for these computing models
- specs to
each stage is more complicated/difficult
- classical approaches can be buttressed with modern ones
- we provide a platform to facilitate
---
# For Each step
- scalability
- quality
- features
- 1-clickiness
### Old and new both important
---
# Answering Scientific Questions from Big Data
1. Look
1. Visualize
2. Download
3. Upload
1. Pre-Process
4. Volume Reconstruct
1. Histogram Normalize
1. Register to Atlas
1. Annotate
1. Label
1. Train
1. Overlay
2. Proofread
1. Assess
1. Deploy
1. Analyze
1. Query
1. Estimate
1. Model Check
---
---
# Appreciation
# Look
| the old | the new |
|--- | --- |
| test | test |
</textarea>
<script src="https://gnab.github.io/remark/downloads/remark-latest.min.js">
</script>
<script>
var slideshow = remark.create();
</script>
</body>
</html>