-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathfeatured-project-voluba.html
243 lines (227 loc) · 10.4 KB
/
featured-project-voluba.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
<!doctype html>
<html>
<head>
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-ZSP3HV4M1C"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-ZSP3HV4M1C');
</script>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-145481065-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-145481065-1');
</script>
<link rel="apple-touch-icon" sizes="180x180" href="favicon/apple-touch-icon.png">
<link rel="icon" type="image/png" sizes="32x32" href="favicon/favicon-32x32.png">
<link rel="icon" type="image/png" sizes="16x16" href="favicon/favicon-16x16.png">
<link rel="manifest" href="favicon/site.webmanifest">
<link rel="mask-icon" href="favicon/safari-pinned-tab.svg" color="#5bbad5">
<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.8.2/css/all.css" integrity="sha384-oS3vJWv+0UjzBfQzYUhtDYW+Pj2yciDJxpsK1OYPAYjqT085Qq/1cq5FLXAZQ7Ay" crossorigin="anonymous">
<meta name="msapplication-TileColor" content="#da532c">
<meta name="theme-color" content="#ffffff">
<meta name="author" content="Derek Lo @ 3design-dlo.com">
<!-- general -->
<link rel="stylesheet" type="text/css" href="css/styles.css" />
<link rel="stylesheet" type="text/css" href="css/timeline.css" />
<link rel="stylesheet" type="text/css" href="css/nav-styles.css" />
<link rel="stylesheet" type="text/css" href="fonts/fonts.css" />
<link href="css/lightbox.css" rel="stylesheet" />
<meta charset="utf-8">
<title>the BigBrain</title>
<meta name="viewport" content="width=device-width">
<meta name="description" content="This is the reference page of the website of the BigBrain Project.">
<meta name="keywords" content="Neuro, Brain, Research, Big Data, Science, Medicine">
<script src="https://code.jquery.com/jquery-1.10.2.js"></script>
<script type="text/javascript" src="js/drop-down.js"></script>
<script src="js/jquery.matchHeight.js" type="text/javascript"></script>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.5.2/css/all.min.css">
</head>
<body>
<div id="main-wrapper">
<div class="social-media">
<a href="https://www.youtube.com/@bigbrainproject" class="tooltip">
<i class="fab fa-youtube"></i>
<span class="tooltiptext">Youtube</span>
</a>
<a href="https://twitter.com/BigBrainProject" class="tooltip">
<i class="fab fa-x-twitter"></i>
<span class="tooltiptext">X</span>
</a>
<a href="https://www.linkedin.com/company/bigbrainproject?trk=public_post_feed-actor-name" class="tooltip">
<i class="fa-brands fa-linkedin-in"></i>
<span class="tooltiptext">linkedin</span>
</a>
<a href="mailto:[email protected]" class="tooltip">
<i class="fas fa-envelope-square"></i>
<span class="tooltiptext">Email</span>
</a>
<a href="#main-wrapper" class="tooltip">
<i class="fas fa-arrow-up"></i>
<span class="tooltiptext">Top</span>
</a>
</div>
<!-- navigation -->
<nav class="site-nav">
<div class="brand-border-1"></div>
<div class="brand-border-2"></div>
<div class="brand-border-3"></div>
<div class="nav-container">
<div class="branding"><a href="index.html">BigBrain Project</a></div>
<div id="showmenu">Menu</div>
<ul id="menu" class="nav-list hide">
<li class="nav-item"><a href="#!"><strong>HIBALL</strong></a>
<ul class="nav-dropdown">
<li><a href="hiball.html">About Hiball</a></li>
<li><a href="board.html">Boards</a></li>
<li><a href="partners.html">Partners</a></li>
<li><a href="publications.html">Publications</a></li>
</ul>
</li>
<li class="nav-item"><a href="#!">About</a>
<ul class="nav-dropdown">
<li><a href="about.html">About Us</a></li>
<li><a href="about.html#FAQ">FAQ</a></li>
<li><a href="press.html">Press</a></li>
<li><a href="references.html">References</a></li>
<li><a href="contact.html">Contact</a></li>
</ul>
</li>
<li class="nav-item"><a href="maps-and-models.html">Maps & Models</a></li>
<li class="nav-item"><a href="tools-and-services.html">Tools & Services</a></li>
<li class="nav-item"><a href="#!" class="active">Community</a>
<ul class="nav-dropdown">
<li><a href="community.html">Our Community</a></li>
<li><a href="news.html">News & Events</a></li>
<li><a href="featured.html" class="active">Featured</a></li>
<li><a href="https://forum.bigbrainproject.org/">Forum</a></li>
<li><a href="careers.html">Careers</a></li>
</ul>
</li>
</ul>
</div>
</nav>
<!-- references section -->
<section class="extra-pad lt-grey-bg">
<div class="section-content end white-bg font-big">
<h1 class="full-width text-center">Featured Project</h1>
<h2 class="full-width text-center">voluba – Interactive registration of high-resolution volumes to 3D reference atlases</h2>
<div class="col-2 internal-padding">
<p>A common problem in high-resolution brain atlasing is spatial anchoring of volumes of interest from imaging experiments into the anatomical context of an ultrahigh-resolution reference model like BigBrain. This process requires efficient 3D interaction with image volumes at the Terabyte scale. We developed the interactive volumetric alignment tool voluba, which is implemented as a web service and offers an intuitive interactive workflow:</p>
<ul class="big-head-space">Check out voluba under the following links. We are also happy to discuss with you on GitHub!
<li><a href="https://voluba.apps.hbp.eu/#/">voluba</a></li>
<li><a href="https://voluba.readthedocs.io/en/latest/">voluba documentation</a></li>
<li><a href="https://github.com/FZJ-INM1-BDA/voluba">voluba on GitHub </a></li>
</ul>
<div class="clear-all"></div>
</div>
<div class="col-2 internal-padding">
<div class="icon-left">
<img src="images/featured/icon-5.png">
</div>
<div class="content-right">
<p><strong>Select reference space and input volume</strong><br>
Choose between BigBrain, Allen mouse or Waxholm rat reference volumes, and upload your own input image after authenticating via EBRAINS or ORCID.
</p>
</div>
<div class="clear-all"></div>
<div class="icon-left">
<img src="images/featured/icon-4.png">
</div>
<div class="content-right">
<p><strong>Adjust the appearance of the input image </strong><br>
Customize contrast, brightness, colormaps, and intensity thresholds of the input image for optimal visualization.
</p>
</div>
<div class="clear-all"></div>
<div class="icon-left">
<img src="images/featured/icon-3.png">
</div>
<div class="content-right">
<p><strong>Interactive Alignment</strong><br>
Manipulate position and orientation of the input volume using the mouse pointer and adjust global parameters including voxel scaling and axis orientations to obtain a 3D similarity transformation.
</p>
</div>
<div class="clear-all"></div>
<div class="icon-left">
<img src="images/featured/icon-2.png">
</div>
<div class="content-right">
<p><strong>Refine With 3D Landmarks</strong><br>
Refine the alignment using interactive annotation of 3D landmark pairs to recalculate the transformation, with additional degrees of freedom including shearing.
</p>
</div>
<div class="clear-all"></div>
<div class="icon-left">
<img src="images/featured/icon-1.png">
</div>
<div class="content-right">
<ul><strong>Use The Results</strong>
<li>Save and reimport transformation and landmarks</li>
<li>Import the result in other tools, such as ANTs</li>
<li>Share a private URL to the anchored volume</li>
<li>Open the anchored volume in the 3D atlas viewer siibra-explorer</li>
</ul>
<p></p>
</div>
<div class="clear-all"></div>
</div>
<div class="clear-all">
<img src="images/featured/voluba.png">
voluba was developed at the Institute of Neuroscience and Medicine (INM-1) at Forschungszentrum Jülich and is available under the Apache2 license and received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).
</div>
</section>
<div class="clear-all"></div>
<!-- footer -->
<footer>
<blockquote class="quote-holder">
<img class="quote-image" src="images/icon-aquisition.png">
<p class="quote-text">Share your projects on <a href="https://forum.bigbrainproject.org/">Discourse</a></p>
</blockquote>
<div class="section-content flex">
<a href="https://www.fz-juelich.de/">
<img src="images/logo-julich.jpg">
</a>
<a href="https://mcgill.ca/">
<img src="images/logo-mcgill.png">
</a>
</div>
<p class="center" style="color: #fff;">For information please email us at <a href="mailto:[email protected]">[email protected]</a><br>All images on this website are licensed <a href="https://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA”</a></p>
</footer>
<div class="brand-border-1"></div>
<div class="brand-border-2"></div>
<div class="brand-border-3"></div>
</div>
<!-- <script>
$(document).ready(function() {
$('#showmenu').click(function() {
$('.nav-list').toggleClass("hide");
});
});
</script> -->
<script>
$(function(){
$(".accordian h3").click(function(e){
$(".accordian ul p.answer").slideUp();
if ($(this).next().is(":hidden")){
$(this).next().slideDown();
}
});
});
</script>
<script>
$(function(){
$("#showmenu").click(function(e){
$("#menu").slideUp();
if ($(this).next().is(":hidden")){
$(this).next().slideDown();
}
});
});
</script>
</body></html>