-
Notifications
You must be signed in to change notification settings - Fork 3
/
index-spatialomics.html
264 lines (194 loc) · 12.8 KB
/
index-spatialomics.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
<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</title>
<meta property="og:title" content="" />
<meta property="og:description" content="" />
<meta property="og:image" content="/assets/media/galaxy-eu-logo.512.png" />
<meta name="description" content="The European Galaxy Instance">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<link rel="stylesheet" href="/assets/css/bootstrap.min.css">
<link rel="stylesheet" href="/assets/css/main.css">
<link rel="canonical" href="https://galaxyproject.eu/index-spatialomics.html">
<link rel="shortcut icon" href="/assets/media/galaxy-eu-logo.64.png" type="image/x-icon" />
<link rel="alternate" type="application/rss+xml" title="Galaxy Europe" href="/feed.xml">
<link href="/assets/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous">
<script src="/assets/js/jquery-3.2.1.slim.min.js" integrity="sha256-k2WSCIexGzOj3Euiig+TlR8gA0EmPjuc79OEeY5L45g=" crossorigin="anonymous"></script>
<script src="/assets/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<h1 class="no_toc" id="welcome-to-the-spatial-omics-galaxy-subdomain-server">Welcome to the Spatial OMICS Galaxy subdomain server</h1>
<p><img src="/assets/media/spatial_omics_banner.jpg" alt="" /></p>
<p>The SpatialOMICS Galaxy subdomain serves as a hub for all tools related to the analysis of highly-multiplexed image analysis. This server currently features the individual components of the <a href="https://mcmicro.org/">MCMICRO</a> pipeline, including <a href="https://github.com/ohsu-comp-bio/basic-illumination">BaSiC</a> for illumination correction, <a href="https://github.com/ohsu-comp-bio/ashlar">ASHLAR</a> for stitching and registration, <a href="https://github.com/ohsu-comp-bio/UNetCoreograph">Coreograph</a> to dearray tissue microarrays (TMAs), <a href="https://github.com/ohsu-comp-bio/UnMicst">UnMICST</a> to create cell or nucleai probability maps, <a href="https://github.com/ohsu-comp-bio/S3segmenter">S3segmenter</a> for nucleai and cell segmentation and <a href="https://github.com/ohsu-comp-bio/quantification">MCQuant</a> for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future.</p>
<p>This subdomain is a collaborative effort and we welcome any suggestions or requests for making tools related to spatia OMICS analysis available on this server. We also welcome contributions to the development of new tools, workflows or trainings!</p>
<h1 class="no_toc" id="content">Content</h1>
<ol id="markdown-toc">
<li><a href="#get-started" id="markdown-toc-get-started">Get started</a></li>
<li><a href="#tools-available" id="markdown-toc-tools-available">Tools available</a> <ol>
<li><a href="#mcmicro-core-tools" id="markdown-toc-mcmicro-core-tools">MCMICRO core tools</a></li>
</ol>
</li>
<li><a href="#workflows-available" id="markdown-toc-workflows-available">Workflows available</a></li>
<li><a href="#contributors" id="markdown-toc-contributors">Contributors</a></li>
</ol>
<h1 id="get-started">Get started</h1>
<p>Are you new to Galaxy, or returning after a long time, and looking for help to get started?
Take <a href="https://spatialomics.usegalaxy.eu/tours/core.galaxy_ui" target="_blank">a guided tour</a> through Galaxy’s user interface.</p>
<h1 id="tools-available">Tools available</h1>
<h2 id="mcmicro-core-tools">MCMICRO core tools</h2>
<p>All of the Galaxy tools for MCMICRO have been developed by the <a href="https://www.ohsu.edu/people/jeremy-goecks-phd">Goecks lab</a> at the <a href="https://github.com/ohsu-comp-bio">Oregon Health and Science University Computational Biology</a>.</p>
<table>
<thead>
<tr>
<th>Tool</th>
<th>Description</th>
<th>Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="https://spatialomics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/" target="_top" title="basic_illumination">basic_illumination</a></td>
<td>BaSiC shading correction for use with Ashlar</td>
<td><a href="https://www.nature.com/articles/ncomms14836" target="_blank">Peng et al. 2017</a></td>
</tr>
<tr>
<td><a href="https://spatialomics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/" target="_top" title="ashlar">ashlar</a></td>
<td>ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration</td>
<td><a href="https://www.biorxiv.org/content/10.1101/2021.04.20.440625v1.full" target="_blank">Muhlich et al. 2021</a></td>
</tr>
<tr>
<td><a href="https://spatialomics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/" target="_top" title="coreograph">coreograph</a></td>
<td>Dearray of Tissue Microarrays</td>
<td><a href="https://github.com/ohsu-comp-bio/UNetCoreograph" target="_blank">Coreograph Github</a></td>
</tr>
<tr>
<td><a href="https://spatialomics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/perssond/unmicst/unmicst/" target="_top" title="unmicst">unmicst</a></td>
<td>UnMICST - Universal Models for Identifying Cells and Segmenting Tissue</td>
<td><a href="https://labsyspharm.github.io/UnMICST-info/" target="_blank">UnMICST info</a></td>
</tr>
<tr>
<td><a href="https://spatialomics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/perssond/s3segmenter/s3segmenter/" target="_top" title="s3segmenter">s3segmenter</a></td>
<td>S3segmenter: A Matlab-based set of functions that generates single cell (nuclei and cytoplasm) label masks</td>
<td><a href="https://github.com/HMS-IDAC/S3segmenter" target="_blank">S3Segmenter github</a></td>
</tr>
<tr>
<td><a href="https://spatialomics.usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/" target="_top" title="quantification">quantification</a></td>
<td>MCQuant: Single cell quantification</td>
<td><a href="https://github.com/labsyspharm/quantification#single-cell-quantification" target="_blank">MCQUant github</a></td>
</tr>
</tbody>
</table>
<h1 id="workflows-available">Workflows available</h1>
<p>Two workflows are currently available to process your samples using the MCMICRO Galaxy pipeline:</p>
<p><a href="https://github.com/ohsu-comp-bio/cycIF-galaxy/blob/master/workflows/Galaxy-Workflow-MCMICRO_TMA_v1.0.0.ga">MCMICRO Tissue Microarray Workflow</a></p>
<p><a href="https://github.com/ohsu-comp-bio/cycIF-galaxy/blob/master/workflows/Galaxy-Workflow-MCMICRO_Tissue_v1.0.0.ga">MCMICRO Whole Slide Tissue Workflow</a></p>
<h1 id="contributors">Contributors</h1>
<ul>
<li><a href="https://github.com/FloWuenne">Florian Wünnemann</a></li>
<li><a href="https://github.com/DenisSch">Denis Schapiro</a></li>
<li><a href="https://github.com/bgruening">Bjoern Gruening</a></li>
<li><a href="https://github.com/jgoecks">Jeremy Goecks</a></li>
<li><a href="https://github.com/CameronFRWatson">Cameron Watson</a></li>
<li><a href="https://github.com/alliecreason">Allison Creason</a></li>
</ul>
<h2>Our Data Policy</h2>
<table class="table table-striped">
<thead>
<tr>
<th>Registered Users</th><th>Unregistered Users</th><th>FTP Data</th><th>GDPR Compliance</th>
</tr>
</thead>
<tbody>
<tr>
<td>User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
as they are not deleted by the user. Once marked as deleted the datasets will
be permanently removed within 14 days. If the user "purges" the dataset in the
Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
</td>
<td>Processed data will only be accessible during one browser session, using a
cookie to identify your data. This cookie is not used for any other purposes
(e.g. tracking or analytics).
If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
</td>
<td>Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
</td>
<td>The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.</td>
</tr>
</tbody>
</table>
<!-- <h4>Registered Users</h4>
User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long
as they are not deleted by the user. Once marked as deleted the datasets will
be permanently removed within 14 days. If the user "purges" the dataset in the
Galaxy, it will be removed immediately, permanently.
An <a href="https://docs.google.com/forms/d/e/1FAIpQLSf9w2MOS6KOlu9XdhRSDqWnCDkzoVBqHJ3zH_My4p8D8ZgkIQ/viewform" target="_blank">extended quota can be requested</a>
for a limited time period in special cases.
<h4>Unregistered Users</h4>
Processed data will only be accessible during one browser session, using a
cookie to identify your data. This cookie is not used for any other purposes
(e.g. tracking or analytics).
If UseGalaxy.eu service is not accessed for 90 days, those datasets will be
permanently deleted.
<h4>FTP Data</h4>
Any user data uploaded to our <a href="https://galaxyproject.eu/ftp/">FTP server</a> should be imported into Galaxy as soon
as possible. Data left in FTP folders for more than 3 months, will be deleted.
<h4>GDPR Compliance</h4>
The Galaxy service complies with the EU General Data Protection Regulation
(GDPR). You can read more about this on our
<a href="https://usegalaxy.eu/terms/">Terms and Conditions</a>.
-->
<div>
<iframe style="border: 0px" width="100%" height="150px" src="https://stats.galaxyproject.eu/d-solo/000000034/jobs-dashboard?orgId=1&refresh=1m&panelId=1" ></iframe>
</div>
<div>
<!--<iframe style="border: 0px" width="33%" height="100px" src="https://stats.galaxyproject.eu/d-solo/000000034/jobs-dashboard?orgId=1&refresh=1m&panelId=3" ></iframe>-->
</div>
<div class="row">
<section class="section-content">
<div class="col-md-12">
</div>
</section>
</div>
</div>
</div>
</div>
</div>
<footer class="navbar-default">
<div class="container">
<div class="row">
</div>
<div class="row">
<div class="col-lg-12" style="text-align:center">
<p>UseGalaxy.eu is maintained largely by the <a href="/freiburg/">Freiburg Galaxy Team</a> but also collectively by groups and individuals from across Europe. All of the member sites in this repository contribute to the European Galaxy Project.
For <strong>acknowledgement</strong>, please refer to the <a href="/about">About</a> section.
All content on this site is available under <a href="https://creativecommons.org/share-your-work/public-domain/cc0/">CC0-1.0</a> unless otherwise specified.</p>
</div>
</div>
<div class="row">
<div class="col-lg-12" style="text-align:center">
<ul class="contact-info">
<li><i class="fa fa-github"></i><a href="https://github.com/usegalaxy-eu/website/tree/master/index-spatialomics.md">Edit this page on GitHub</a></li>
<li><i class="fa fa-envelope"></i><a href="mailto:[email protected]">[email protected]</a></li>
<li><i class="fa fa-github"></i><a href="https://github.com/usegalaxy-eu">usegalaxy-eu</a></li>
<li><img class="fa-mastodon" src="/assets/media/mastodon.svg" style="width:18px;height:18px;padding-right:4px;filter:grayscale(100%);-webkit-filter:grayscale(100%);"/><a href="https://bawü.social/@galaxyfreiburg">galaxyfreiburg</a></li>
<li><i class="fa fa-rss"></i>Subscribe <a href="/feed.xml">via RSS (UseGalaxy.eu Feed)</a></li>
</ul>
</div>
</div>
</div>
</footer>
<script async defer data-domain="galaxyproject.eu" src="https://plausible.galaxyproject.eu/js/plausible.js"></script>
</body>
</html>