├── .gitignore ├── LICENSE ├── README.md ├── aux ├── NewExperiment.pdf └── f1.png ├── docs ├── .gitignore ├── .tweet-cache │ ├── 02b591d77a446cb7531ab71b75d3d2bc.cache │ └── f18f38b6b6bb712c5873a899905f747c.cache ├── 404.html ├── Dockerfile.dev ├── Gemfile ├── Gemfile.lock ├── LICENSE ├── _config.yml ├── _data │ ├── authors.yml │ ├── licenses.yml │ ├── locale.yml │ ├── navigation.yml │ └── variables.yml ├── _includes │ ├── analytics-providers │ │ ├── custom.html │ │ └── google.html │ ├── analytics.html │ ├── article-footer.html │ ├── article-header.html │ ├── article-info.html │ ├── article-list.html │ ├── article-section-navigator.html │ ├── article │ │ ├── footer │ │ │ ├── author-profile.html │ │ │ ├── custom.html │ │ │ ├── license.html │ │ │ └── subscribe.html │ │ └── top │ │ │ └── custom.html │ ├── aside │ │ └── toc.html │ ├── author-links.html │ ├── comments-providers │ │ ├── custom.html │ │ ├── disqus.html │ │ ├── gitalk.html │ │ └── valine.html │ ├── comments.html │ ├── extensions │ │ ├── bilibili.html │ │ ├── codepen.html │ │ ├── netease-cloud-music.html │ │ ├── slideshare.html │ │ ├── soundcloud.html │ │ ├── ted.html │ │ └── youtube.html │ ├── footer.html │ ├── head.html │ ├── head │ │ ├── custom.html │ │ └── favicon.html │ ├── header.html │ ├── main │ │ ├── bottom │ │ │ └── custom.html │ │ └── top │ │ │ └── custom.html │ ├── markdown-enhancements.html │ ├── markdown-enhancements │ │ ├── chart.html │ │ ├── mathjax.html │ │ └── mermaid.html │ ├── pageview-providers │ │ ├── custom │ │ │ ├── home.html │ │ │ └── post.html │ │ └── leancloud │ │ │ ├── home.html │ │ │ ├── leancloud.js │ │ │ └── post.html │ ├── pageview.html │ ├── paginator.html │ ├── scripts │ │ ├── archieve.js │ │ ├── article.js │ │ ├── aside │ │ │ ├── affix.js │ │ │ └── toc.js │ │ ├── common.js │ │ ├── components │ │ │ ├── lightbox.js │ │ │ ├── search.js │ │ │ └── sidebar.js │ │ ├── home.js │ │ ├── lib │ │ │ ├── affix.js │ │ │ ├── gallery.js │ │ │ ├── lazyload.js │ │ │ ├── modal.js │ │ │ ├── scroll-to.js │ │ │ ├── swiper.js │ │ │ ├── throttle.js │ │ │ └── toc.js │ │ ├── page.js │ │ ├── utils │ │ │ ├── imagesLoad.js │ │ │ └── utils.js │ │ └── variables.html │ ├── search-providers │ │ ├── custom │ │ │ └── search.html │ │ ├── default │ │ │ ├── search-data.js │ │ │ ├── search.html │ │ │ └── search.js │ │ └── google-custom-search-engine │ │ │ ├── search.html │ │ │ └── search.js │ ├── search.html │ ├── sharing-providers │ │ ├── addthis.html │ │ ├── addtoany.html │ │ └── custom.html │ ├── sharing.html │ ├── sidebar │ │ └── toc.html │ ├── snippets │ │ ├── assign.html │ │ ├── get-article-title.html │ │ ├── get-lang.html │ │ ├── get-locale-string.html │ │ ├── get-nav-url.html │ │ ├── get-sources.html │ │ ├── get-string-from-locale-config.html │ │ ├── is_collection.html │ │ ├── page-url.html │ │ ├── prepend-baseurl.html │ │ └── prepend-path.html │ ├── svg │ │ ├── icon │ │ │ └── social │ │ │ │ ├── behance.svg │ │ │ │ ├── douban.svg │ │ │ │ ├── facebook.svg │ │ │ │ ├── flicker.svg │ │ │ │ ├── github.svg │ │ │ │ ├── googleplus.svg │ │ │ │ ├── linkedin.svg │ │ │ │ ├── mail.svg │ │ │ │ ├── medium.svg │ │ │ │ ├── npm.svg │ │ │ │ ├── pinterest.svg │ │ │ │ ├── qq.svg │ │ │ │ ├── telegram.svg │ │ │ │ ├── twitter.svg │ │ │ │ ├── weibo.svg │ │ │ │ ├── weixin.svg │ │ │ │ └── zhihu.svg │ │ └── logo.svg │ └── tags.html ├── _layouts │ ├── 404.html │ ├── archive.html │ ├── article.html │ ├── articles.html │ ├── base.html │ ├── home.html │ ├── landing.html │ ├── none.html │ └── page.html ├── _sass │ ├── additional │ │ ├── _alert.scss │ │ ├── _photo-frame.scss │ │ └── _tag.scss │ ├── animate │ │ ├── _fade-in-down.scss │ │ ├── _fade-in-up.scss │ │ └── _fade-in.scss │ ├── common │ │ ├── _classes.scss │ │ ├── _function.scss │ │ ├── _print.scss │ │ ├── _reset.scss │ │ ├── _variables.scss │ │ ├── classes │ │ │ ├── _animation.scss │ │ │ ├── _clearfix.scss │ │ │ ├── _clickable.scss │ │ │ ├── _display.scss │ │ │ ├── _flex.scss │ │ │ ├── _grid.scss │ │ │ ├── _horizontal-rules.scss │ │ │ ├── _link.scss │ │ │ ├── _media.scss │ │ │ ├── _overflow.scss │ │ │ ├── _pseudo.scss │ │ │ ├── _shadow.scss │ │ │ ├── _spacing.scss │ │ │ ├── _split-line.scss │ │ │ ├── _text.scss │ │ │ ├── _transform.scss │ │ │ ├── _transition.scss │ │ │ └── _user-select.scss │ │ └── components │ │ │ ├── _button.scss │ │ │ ├── _card.scss │ │ │ ├── _gallery.scss │ │ │ ├── _hero.scss │ │ │ ├── _image.scss │ │ │ ├── _item.scss │ │ │ ├── _menu.scss │ │ │ ├── _modal.scss │ │ │ ├── _swiper.scss │ │ │ └── _toc.scss │ ├── components │ │ ├── _article-content.scss │ │ ├── _article-footer.scss │ │ ├── _article-header.scss │ │ ├── _article-info.scss │ │ ├── _article-list.scss │ │ ├── _author-links.scss │ │ ├── _author-profile.scss │ │ ├── _extensions.scss │ │ ├── _footer.scss │ │ ├── _header.scss │ │ ├── _lightbox.scss │ │ ├── _main.scss │ │ ├── _search.scss │ │ └── _tags.scss │ ├── custom.scss │ ├── layout │ │ ├── _404.scss │ │ ├── _archive.scss │ │ ├── _article.scss │ │ ├── _articles.scss │ │ ├── _base.scss │ │ ├── _home.scss │ │ ├── _landing.scss │ │ └── _page.scss │ └── skins │ │ ├── _chocolate.scss │ │ ├── _dark.scss │ │ ├── _default.scss │ │ ├── _forest.scss │ │ ├── _ocean.scss │ │ ├── _orange.scss │ │ └── highlight │ │ ├── _default.scss │ │ ├── _tomorrow-night-blue.scss │ │ ├── _tomorrow-night-bright.scss │ │ ├── _tomorrow-night-eighties.scss │ │ ├── _tomorrow-night.scss │ │ ├── _tomorrow.scss │ │ └── tomorrow │ │ ├── _default.scss │ │ ├── _highlight.scss │ │ ├── _night-blue.scss │ │ ├── _night-bright.scss │ │ ├── _night-eighties.scss │ │ └── _night.scss ├── archive.html ├── assets │ ├── android-chrome-192x192.png │ ├── android-chrome-256x256.png │ ├── apple-touch-icon.png │ ├── browserconfig.xml │ ├── css │ │ └── main.scss │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon.ico │ ├── images │ │ └── logo │ │ │ └── logo.svg │ ├── mstile-150x150.png │ ├── search.js │ └── site.webmanifest ├── docker │ ├── docker-compose.build-image.yml │ ├── docker-compose.default.yml │ ├── docker-compose.demo.yml │ ├── docker-compose.dev.yml │ ├── docker-compose.prod.yml │ └── nginx.conf ├── docs │ ├── 00_about.md │ ├── 01-make-meta.md │ ├── 02-check_image.md │ ├── 03-crop-image.md │ ├── 04-gene-exp-hvg.md │ ├── 05_clip_human_brain_DLPFC.md │ ├── 06_plip_human_brain_DLPFC.md │ ├── 07-linear_probing.md │ ├── 08-embedding_score.md │ ├── 09_for_new_to_ST.md │ ├── 10_ST_analysis_quick_start.md │ ├── 11-gene-exp-prediction.md │ ├── 12-segmentation.md │ ├── 13-code-for_figs.md │ ├── doc_data │ │ ├── Michael_Hooker_Research_Center_Zoom_Background_2.jpg │ │ ├── UNC_logo_RGB.png │ │ ├── f1.png │ │ └── model_st.py │ └── landing.html ├── favicon.ico ├── index.html └── jekyll-text-theme.gemspec ├── example ├── Human_Breast_Andersson_10142021_ST_A1.png ├── Human_Breast_Andersson_10142021_ST_A1_coord.csv └── Human_Breast_Andersson_10142021_ST_A1_count.csv ├── meta ├── meta_all_gene.csv └── meta_all_gene02122025.csv └── metadata.json /.gitignore: -------------------------------------------------------------------------------- 1 | 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2024 Jiawen Chen 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # STimage-1K4M Dataset 2 | 3 | Welcome to the STimage-1K4M Dataset repository. This dataset is designed to foster research in the field of spatial transcriptomics, combining high-resolution histopathology images with detailed gene expression data. 4 | 5 |  6 | 7 | ## Update 8 | 9 | ***Feb 12, 2025*** 10 | We corrected a typo in meta file (changed "Human_Brain+Kidney_10X_02212023_Visium" to "Mouse_Brain+Kidney_10X_02212023_Visium"). Please refer to **meta_all_gene02122025.csv** for the newest meta data. 11 | 12 | 13 | ## Dataset Description 14 | 15 | STimage-1K4M consists of 1,149 spatial transcriptomics slides, totaling over 4 million spots with paired gene expression data. This dataset includes: 16 | 17 | - Images. 18 | - Gene expression profiles matched with high-resolution histopathology images. 19 | - Spatial coordinates for each spot. 20 | 21 | See example folder for an example slide from Andersson et al. (pmid: 34650042). 22 | 23 | ## Getting Started 24 | 25 | To use the STimage-1K4M dataset in your research, please access the dataset via [Hugging Face](https://huggingface.co/datasets/jiawennnn/STimage-1K4M). 26 | 27 | ## Data structure 28 | The data structure is organized as follows: 29 | 30 | ```bash 31 | ├── annotation # Pathologist annotation 32 | ├── meta # Test files (alternatively `spec` or `tests`) 33 | │ ├── bib.txt # the bibtex for all studies with pmid included in the dataset 34 | │ ├── meta_all_gene.csv # The meta information 35 | ├── ST # Include all data for tech: Spatial Transcriptomics 36 | │ ├── coord # Include the spot coordinates & spot radius of each slide 37 | │ ├── gene_exp # Include the gene expression of each slide 38 | │ └── image # Include the image each slide 39 | ├── Visium # Include all data for tech: Visium, same structure as ST 40 | ├── VisiumHD # Include all data for tech: VisiumHD, same structure as ST 41 | ``` 42 | ## Repository structure 43 | 44 | The code for data processing and reproducing evaluation result in the paper are in [Document](https://jiawenchenn.github.io/STimage-1K4M/docs/01-make-meta). 45 | 46 | ## Acknowledgement 47 | The fine-tuning and evaluation codes borrows heavily from [CLIP](https://github.com/openai/CLIP/issues/83) and [PLIP](https://github.com/PathologyFoundation/plip/). 48 | 49 | ## Citation 50 | 51 | ``` 52 | 53 | @inproceedings{NEURIPS2024_3ef2b740, 54 | author = {Chen, Jiawen and Zhou, Muqing and Wu, Wenrong and Zhang, Jinwei and Li, Yun and Li, Didong}, 55 | booktitle = {Advances in Neural Information Processing Systems}, 56 | editor = {A. Globerson and L. Mackey and D. Belgrave and A. Fan and U. Paquet and J. Tomczak and C. Zhang}, 57 | pages = {35796--35823}, 58 | publisher = {Curran Associates, Inc.}, 59 | title = {STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics}, 60 | url = {https://proceedings.neurips.cc/paper_files/paper/2024/file/3ef2b740cb22dcce67c20989cb3d3fce-Paper-Datasets_and_Benchmarks_Track.pdf}, 61 | volume = {37}, 62 | year = {2024} 63 | } 64 | 65 | ``` 66 | 67 | ## License 68 | 69 | All code is licensed under the MIT License - see the LICENSE.md file for details. 70 | -------------------------------------------------------------------------------- /aux/NewExperiment.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JiawenChenn/STimage-1K4M/856ea1357d1951c343536d091dac081cb13c3d4f/aux/NewExperiment.pdf -------------------------------------------------------------------------------- /aux/f1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JiawenChenn/STimage-1K4M/856ea1357d1951c343536d091dac081cb13c3d4f/aux/f1.png -------------------------------------------------------------------------------- /docs/.gitignore: -------------------------------------------------------------------------------- 1 | _site 2 | .sass-cache 3 | .jekyll-cache 4 | .jekyll-metadata 5 | vendor 6 | -------------------------------------------------------------------------------- /docs/.tweet-cache/02b591d77a446cb7531ab71b75d3d2bc.cache: -------------------------------------------------------------------------------- 1 | {"url":"https://twitter.com/rubygems/status/518821243320287232","author_name":"RubyGems","author_url":"https://twitter.com/rubygems","html":"
\n\n\n","width":550,"height":null,"type":"rich","cache_age":"3153600000","provider_name":"Twitter","provider_url":"https://twitter.com","version":"1.0"} -------------------------------------------------------------------------------- /docs/.tweet-cache/f18f38b6b6bb712c5873a899905f747c.cache: -------------------------------------------------------------------------------- 1 | {"url":"https://twitter.com/jekyllrb","title":"","html":"Tweets by jekyllrb\n\n","width":500,"height":null,"type":"rich","cache_age":"3153600000","provider_name":"Twitter","provider_url":"https://twitter.com","version":"1.0"} -------------------------------------------------------------------------------- /docs/404.html: -------------------------------------------------------------------------------- 1 | --- 2 | layout: 404 3 | --- 4 | -------------------------------------------------------------------------------- /docs/Dockerfile.dev: -------------------------------------------------------------------------------- 1 | FROM ruby:2.7 2 | 3 | # Set default locale for the environment 4 | ENV LC_ALL C.UTF-8 5 | ENV LANG en_US.UTF-8 6 | ENV LANGUAGE en_US.UTF-8 7 | 8 | # throw errors if Gemfile has been modified since Gemfile.lock 9 | RUN bundle config --global frozen 1 10 | 11 | WORKDIR /usr/src/app 12 | 13 | COPY Gemfile Gemfile.lock jekyll-text-theme.gemspec ./ 14 | RUN bundle install 15 | 16 | EXPOSE 4000 17 | 18 | CMD ["bundle", "exec", "jekyll", "help"] 19 | -------------------------------------------------------------------------------- /docs/Gemfile: -------------------------------------------------------------------------------- 1 | source "https://rubygems.org" 2 | 3 | # gem "github-pages", group: :jekyll_plugins 4 | gemspec 5 | -------------------------------------------------------------------------------- /docs/LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2017 Tian Qi 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /docs/_data/authors.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JiawenChenn/STimage-1K4M/856ea1357d1951c343536d091dac081cb13c3d4f/docs/_data/authors.yml -------------------------------------------------------------------------------- /docs/_data/licenses.yml: -------------------------------------------------------------------------------- 1 | CC-BY-4.0: 2 | name: Attribution 4.0 International 3 | url: https://creativecommons.org/licenses/by/4.0/ 4 | image: https://i.creativecommons.org/l/by/4.0/88x31.png 5 | CC-BY-SA-4.0: 6 | name: Attribution-ShareAlike 4.0 International 7 | url: https://creativecommons.org/licenses/by-sa/4.0/ 8 | image: https://i.creativecommons.org/l/by-sa/4.0/88x31.png 9 | CC-BY-NC-4.0: 10 | name: Attribution-NonCommercial 4.0 International 11 | url: https://creativecommons.org/licenses/by-nc/4.0/ 12 | image: https://i.creativecommons.org/l/by-nc/4.0/88x31.png 13 | CC-BY-ND-4.0: 14 | name: Attribution-NoDerivatives 4.0 International 15 | url: https://creativecommons.org/licenses/by-nd/4.0/ 16 | image: https://i.creativecommons.org/l/by-nd/4.0/88x31.png 17 | -------------------------------------------------------------------------------- /docs/_data/navigation.yml: -------------------------------------------------------------------------------- 1 | header: 2 | 3 | - titles: 4 | # @start locale config 5 | en : &EN About 6 | # @end locale config 7 | url: docs/00_about 8 | 9 | - titles: 10 | # @start locale config 11 | en : &EN Document 12 | # @end locale config 13 | url: docs/01-make-meta 14 | 15 | document_nav: 16 | - title: Data processing 17 | children: 18 | - title: Meta data cleaning 19 | url: docs/01-make-meta 20 | - title: Check spot location 21 | url: docs/02-check_image 22 | - title: Crop spot-level image 23 | url: docs/03-crop-image 24 | - title: Gene expression processing 25 | url: docs/04-gene-exp-hvg 26 | - title: Fine-tuning 27 | children: 28 | - title: Fine-tune CLIP 29 | url: docs/05_clip_human_brain_DLPFC 30 | - title: Fine-tune PLIP 31 | url: docs/06_plip_human_brain_DLPFC 32 | - title: Evaluation 33 | children: 34 | - title: Linear probing 35 | url: docs/07-linear_probing 36 | - title: Image representation learning 37 | url: docs/08-embedding_score 38 | - title: Gene expression prediction 39 | url: docs/11-gene-exp-prediction 40 | - title: Nuclear segmentation 41 | url: docs/12-segmentation 42 | - title: Code for reproducing figures 43 | url: docs/13-code-for_figs 44 | - title: Resources 45 | children: 46 | - title: Intro to ST technology 47 | url: docs/09_for_new_to_ST 48 | - title: ST data analysis quick start 49 | url: docs/10_ST_analysis_quick_start 50 | -------------------------------------------------------------------------------- /docs/_data/variables.yml: -------------------------------------------------------------------------------- 1 | default: 2 | text_skin: default 3 | highlight_theme: default 4 | lang: en 5 | paths: 6 | root: / 7 | home: / 8 | archive: /archive.html 9 | rss: /feed.xml 10 | mathjax: false 11 | mathjax_autoNumber: false 12 | mermaid: false 13 | chart: false 14 | toc: 15 | selectors: 'h1,h2,h3' 16 | sources: bootcdn 17 | 18 | page: 19 | mode: normal 20 | type: webpage 21 | article_header: 22 | align: left 23 | theme: light 24 | articles: 25 | show_cover: true 26 | show_excerpt: false 27 | show_readmore: false 28 | show_info: false 29 | show_title: true 30 | show_edit_on_github: false 31 | show_date: true 32 | show_tags: true 33 | show_author_profile: false 34 | show_subscribe: false 35 | full_width: false 36 | sharing: false 37 | comment: true 38 | license: false 39 | pageview: false 40 | search: default 41 | 42 | sources: 43 | bootcdn: 44 | font_awesome: 'https://cdn.bootcdn.net/ajax/libs/font-awesome/5.15.1/css/all.css' 45 | jquery: 'https://cdn.bootcss.com/jquery/3.1.1/jquery.min.js' 46 | leancloud_js_sdk: '//cdn.jsdelivr.net/npm/leancloud-storage@3.13.2/dist/av-min.js' 47 | chart: 'https://cdn.bootcss.com/Chart.js/2.7.2/Chart.bundle.min.js' 48 | gitalk: 49 | js: 'https://cdn.bootcss.com/gitalk/1.2.2/gitalk.min.js' 50 | css: 'https://cdn.bootcss.com/gitalk/1.2.2/gitalk.min.css' 51 | valine: 'https://unpkg.com/valine/dist/Valine.min.js' # bootcdn not available 52 | mathjax: 'https://cdn.bootcss.com/mathjax/2.7.4/MathJax.js?config=TeX-MML-AM_CHTML' 53 | mermaid: 'https://cdn.bootcss.com/mermaid/8.0.0-rc.8/mermaid.min.js' 54 | unpkg: 55 | font_awesome: 'https://use.fontawesome.com/releases/v5.15.1/css/all.css' 56 | jquery: 'https://unpkg.com/jquery@3.3.1/dist/jquery.min.js' 57 | leancloud_js_sdk: '//cdn.jsdelivr.net/npm/leancloud-storage@3.13.2/dist/av-min.js' 58 | chart: 'https://unpkg.com/chart.js@2.7.2/dist/Chart.min.js' 59 | gitalk: 60 | js: 'https://unpkg.com/gitalk@1.2.2/dist/gitalk.min.js' 61 | css: 'https://unpkg.com/gitalk@1.2.2/dist/gitalk.css' 62 | valine: 'https//unpkg.com/valine/dist/Valine.min.js' 63 | mathjax: 'https://unpkg.com/mathjax@2.7.4/unpacked/MathJax.js?config=TeX-MML-AM_CHTML' 64 | mermaid: 'https://unpkg.com/mermaid@8.0.0-rc.8/dist/mermaid.min.js' 65 | -------------------------------------------------------------------------------- /docs/_includes/analytics-providers/custom.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | -------------------------------------------------------------------------------- /docs/_includes/analytics-providers/google.html: -------------------------------------------------------------------------------- 1 | {%- if site.analytics.google.tracking_id -%} 2 | 3 | 4 | 14 | {%- endif -%} 15 | -------------------------------------------------------------------------------- /docs/_includes/analytics.html: -------------------------------------------------------------------------------- 1 | {%- if jekyll.environment != 'development' -%} 2 | {%- if site.analytics.provider == 'google' -%} 3 | {%- include analytics-providers/google.html -%} 4 | {%- elsif site.analytics.provider == 'custom' -%} 5 | {%- include analytics-providers/custom.html -%} 6 | {%- endif -%} 7 | {%- endif -%} 8 | -------------------------------------------------------------------------------- /docs/_includes/article-footer.html: -------------------------------------------------------------------------------- 1 | {%- include snippets/assign.html 2 | target=site.data.variables.default.page.show_author_profile 3 | source0=layout.show_author_profile source1=page.show_author_profile -%} 4 | {%- assign _show_author_profile = __return -%} 5 | 6 | {%- include snippets/assign.html 7 | target=site.data.variables.default.page.show_subscribe 8 | source0=layout.show_subscribe source1=page.show_subscribe -%} 9 | {%- assign _show_subscribe = __return -%} 10 | 11 | {%- include snippets/assign.html 12 | target=site.data.variables.default.page.license 13 | source0=layout.license source1=page.license -%} 14 | {%- assign _license = __return -%} 15 | 16 | 56 | -------------------------------------------------------------------------------- /docs/_includes/article-header.html: -------------------------------------------------------------------------------- 1 | {%- include snippets/get-article-title.html article=include.article-%} 2 | {%- assign _article_title = __return -%} 3 | 4 | {%- if include.html != false -%} 5 | 6 | {%- include snippets/assign.html 7 | target=site.data.variables.default.page.show_title 8 | source0=layout.show_title source1=include.article.show_title -%} 9 | {%- assign _show_title = __return -%} 10 | 11 | {%- include snippets/assign.html 12 | target=site.data.variables.default.page.show_edit_on_github 13 | source0=layout.show_edit_on_github source1=include.article.show_edit_on_github -%} 14 | {%- assign _show_edit_on_github = __return -%} 15 | 16 | {%- if _show_title or _show_edit_on_github -%} 17 |jekyll-twitter-plugin (1.0.0): A Liquid tag plugin for Jekyll that renders Tweets from Twitter API http://t.co/m4EIQPM9h4
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