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Add NimbusImage publication
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‎docs/Gemfile.lock‎

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GEM
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remote: https://rubygems.org/
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specs:
4-
activesupport (7.1.3.4)
4+
activesupport (7.2.3)
55
base64
6+
benchmark (>= 0.3)
67
bigdecimal
7-
concurrent-ruby (~> 1.0, >= 1.0.2)
8+
concurrent-ruby (~> 1.0, >= 1.3.1)
89
connection_pool (>= 2.2.5)
910
drb
1011
i18n (>= 1.6, < 2)
12+
logger (>= 1.4.2)
1113
minitest (>= 5.1)
12-
mutex_m
13-
tzinfo (~> 2.0)
14-
addressable (2.8.7)
15-
public_suffix (>= 2.0.2, < 7.0)
16-
base64 (0.2.0)
17-
bigdecimal (3.1.8)
14+
securerandom (>= 0.3)
15+
tzinfo (~> 2.0, >= 2.0.5)
16+
addressable (2.8.8)
17+
public_suffix (>= 2.0.2, < 8.0)
18+
base64 (0.3.0)
19+
benchmark (0.5.0)
20+
bigdecimal (3.3.1)
1821
bulma-clean-theme (0.14.0)
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jekyll (>= 3.9, < 5.0)
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jekyll-feed (~> 0.15)
@@ -27,33 +30,37 @@ GEM
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execjs
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coffee-script-source (1.12.2)
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colorator (1.1.0)
30-
commonmarker (0.23.10)
31-
concurrent-ruby (1.3.4)
32-
connection_pool (2.4.1)
33-
dnsruby (1.72.2)
33+
commonmarker (0.23.12)
34+
concurrent-ruby (1.3.5)
35+
connection_pool (2.5.5)
36+
csv (3.3.5)
37+
dnsruby (1.73.1)
38+
base64 (>= 0.2)
39+
logger (~> 1.6)
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simpleidn (~> 0.2.1)
35-
drb (2.2.1)
41+
drb (2.2.3)
3642
em-websocket (0.5.3)
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eventmachine (>= 0.12.9)
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http_parser.rb (~> 0)
39-
ethon (0.16.0)
45+
ethon (0.15.0)
4046
ffi (>= 1.15.0)
4147
eventmachine (1.2.7)
42-
execjs (2.9.1)
43-
faraday (2.8.1)
44-
base64
45-
faraday-net_http (>= 2.0, < 3.1)
46-
ruby2_keywords (>= 0.0.4)
47-
faraday-net_http (3.0.2)
48-
ffi (1.17.0)
48+
execjs (2.10.0)
49+
faraday (2.14.0)
50+
faraday-net_http (>= 2.0, < 3.5)
51+
json
52+
logger
53+
faraday-net_http (3.4.2)
54+
net-http (~> 0.5)
55+
ffi (1.17.2-x86_64-linux-musl)
4956
forwardable-extended (2.6.0)
5057
gemoji (4.1.0)
51-
github-pages (231)
58+
github-pages (232)
5259
github-pages-health-check (= 1.18.2)
53-
jekyll (= 3.9.5)
60+
jekyll (= 3.10.0)
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jekyll-avatar (= 0.8.0)
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jekyll-coffeescript (= 1.2.2)
56-
jekyll-commonmark-ghpages (= 0.4.0)
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jekyll-commonmark-ghpages (= 0.5.1)
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jekyll-default-layout (= 0.1.5)
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jekyll-feed (= 0.17.0)
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jekyll-gist (= 1.5.0)
@@ -90,9 +97,10 @@ GEM
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liquid (= 4.0.4)
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mercenary (~> 0.3)
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minima (= 2.5.1)
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nokogiri (>= 1.13.6, < 2.0)
100+
nokogiri (>= 1.16.2, < 2.0)
94101
rouge (= 3.30.0)
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terminal-table (~> 1.4)
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webrick (~> 1.8)
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github-pages-health-check (1.18.2)
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addressable (~> 2.3)
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dnsruby (~> 1.60)
@@ -103,11 +111,12 @@ GEM
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activesupport (>= 2)
104112
nokogiri (>= 1.4)
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http_parser.rb (0.8.0)
106-
i18n (1.14.5)
114+
i18n (1.14.7)
107115
concurrent-ruby (~> 1.0)
108-
jekyll (3.9.5)
116+
jekyll (3.10.0)
109117
addressable (~> 2.4)
110118
colorator (~> 1.0)
119+
csv (~> 3.0)
111120
em-websocket (~> 0.5)
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i18n (>= 0.7, < 2)
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jekyll-sass-converter (~> 1.0)
@@ -118,16 +127,17 @@ GEM
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pathutil (~> 0.9)
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rouge (>= 1.7, < 4)
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safe_yaml (~> 1.0)
130+
webrick (>= 1.0)
121131
jekyll-avatar (0.8.0)
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jekyll (>= 3.0, < 5.0)
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jekyll-coffeescript (1.2.2)
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coffee-script (~> 2.2)
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coffee-script-source (~> 1.12)
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jekyll-commonmark (1.4.0)
127137
commonmarker (~> 0.22)
128-
jekyll-commonmark-ghpages (0.4.0)
129-
commonmarker (~> 0.23.7)
130-
jekyll (~> 3.9.0)
138+
jekyll-commonmark-ghpages (0.5.1)
139+
commonmarker (>= 0.23.7, < 1.1.0)
140+
jekyll (>= 3.9, < 4.0)
131141
jekyll-commonmark (~> 1.4.0)
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rouge (>= 2.0, < 5.0)
133143
jekyll-default-layout (0.1.5)
@@ -213,6 +223,7 @@ GEM
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gemoji (>= 3, < 5)
214224
html-pipeline (~> 2.2)
215225
jekyll (>= 3.0, < 5.0)
226+
json (2.16.0)
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kramdown (2.4.0)
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rexml
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kramdown-parser-gfm (1.1.0)
@@ -221,14 +232,16 @@ GEM
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listen (3.9.0)
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rb-fsevent (~> 0.10, >= 0.10.3)
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rb-inotify (~> 0.9, >= 0.9.10)
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logger (1.7.0)
224236
mercenary (0.3.6)
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minima (2.5.1)
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jekyll (>= 3.5, < 5.0)
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jekyll-feed (~> 0.9)
228240
jekyll-seo-tag (~> 2.1)
229-
minitest (5.25.1)
230-
mutex_m (0.2.0)
231-
nokogiri (1.18.9-x86_64-linux-gnu)
241+
minitest (5.26.2)
242+
net-http (0.8.0)
243+
uri (>= 0.11.1)
244+
nokogiri (1.18.10-x86_64-linux-musl)
232245
racc (~> 1.4)
233246
octokit (4.25.1)
234247
faraday (>= 1, < 3)
@@ -240,33 +253,35 @@ GEM
240253
rb-fsevent (0.11.2)
241254
rb-inotify (0.11.1)
242255
ffi (~> 1.0)
243-
rexml (3.4.2)
256+
rexml (3.4.4)
244257
rouge (3.30.0)
245-
ruby2_keywords (0.0.5)
246-
rubyzip (2.3.2)
258+
rubyzip (2.4.1)
247259
safe_yaml (1.0.5)
248260
sass (3.7.4)
249261
sass-listen (~> 4.0.0)
250262
sass-listen (4.0.0)
251263
rb-fsevent (~> 0.9, >= 0.9.4)
252264
rb-inotify (~> 0.9, >= 0.9.7)
253-
sawyer (0.9.2)
265+
sawyer (0.9.3)
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addressable (>= 2.3.5)
255267
faraday (>= 0.17.3, < 3)
268+
securerandom (0.4.1)
256269
simpleidn (0.2.3)
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terminal-table (1.8.0)
258271
unicode-display_width (~> 1.1, >= 1.1.1)
259-
typhoeus (1.4.1)
260-
ethon (>= 0.9.0)
272+
typhoeus (1.5.0)
273+
ethon (>= 0.9.0, < 0.16.0)
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tzinfo (2.0.6)
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concurrent-ruby (~> 1.0)
263-
tzinfo-data (1.2024.1)
276+
tzinfo-data (1.2025.2)
264277
tzinfo (>= 1.0.0)
265278
unicode-display_width (1.8.0)
279+
uri (1.1.1)
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wdm (0.1.1)
281+
webrick (1.9.1)
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PLATFORMS
269-
x86_64-linux
284+
x86_64-linux-musl
270285

271286
DEPENDENCIES
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bulma-clean-theme
@@ -276,4 +291,4 @@ DEPENDENCIES
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wdm (~> 0.1.1)
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BUNDLED WITH
279-
2.3.24
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2.3.25

‎docs/papers-publications/index.md‎

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[//]: # (keys are title, full-citation, DOI_link, link, DOI, PMID)
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publications:
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- title: "NimbusImage: A Cloud-Computing Platform for Image Analysis."
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full-citation: "Niu, Zijian, Thibault Bruyère, David Manthey, Jingxin Li, Aoife O’Farrell, and Arjun Raj. 2025. “NimbusImage: A Cloud-Computing Platform for Image Analysis.” Nature Methods, ahead of print, November 20."
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DOI_link: https://doi.org/10.1038/s41592-025-02942-6
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link: https://www.nature.com/articles/s41592-025-02942-6
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DOI: 10.1038/s41592-025-02942-6
22+
PMID: 41266644
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- title: "FUSION: A Web-Based Application for in-Depth Exploration of Multi-Omics Data with Brightfield Histology."
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full-citation: "Border, Samuel P., Ricardo Melo Ferreira, Nicholas Lucarelli, Suhas Katari Chaluva Kumar, Anindya S. Paul, David Manthey, Laura Barisoni, et al. 2025. “FUSION: A Web-Based Application for in-Depth Exploration of Multi-Omics Data with Brightfield Histology.” Nature Communications 16 (1)."
1925
DOI_link: https://doi.org/10.1038/s41467-025-63050-9

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