diff --git a/_quarto.yml b/_quarto.yml index 949e0e4..0cbc52a 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -6,9 +6,9 @@ website: navbar: right: - text: "ImgLib2" - href: "imglib2.qmd" + href: "imglib2" - text: "BDV" - href: "bdv.qmd" + href: "bdv" - text: Blog href: blog.qmd - text: Resources @@ -45,20 +45,26 @@ website: open-graph: true repo-url: https://github.com/imglib/imglib2-www site-url: https://imglib.github.io/imglib2-www - sidebar: - collapse-level: 2 - style: "floating" - search: false - contents: - - section: "ImgLib2" - contents: ImageJ_Documentation/imglib2/* - pinned: false - - section: "ImgLib 'Deprecated' " - contents: ImageJ_Documentation/imglib1/* - pinned: false - tools: - - icon: github - href: https://github.com/imglib/imglib2 + # Sidebar configuration using Hybrid Navigation, as described at: + # https://quarto.org/docs/websites/website-navigation.html#hybrid-navigation + # The intent is for the ImgLib2 section of the site to show all ImgLib2 + # articles in a dedicated sidebar, and similarly, for the BigDataViewer + # section of the site to show all BigDataViewer articles in its sidebar. + sidebar: + - title: "BigDataViewer" + style: "docked" + background: light + collapse-level: 2 + contents: + - bdv/index.qmd + - auto: "bdv/*" + - title: "ImgLib2" + style: "docked" + background: light + collapse-level: 2 + contents: + - imglib2/index.qmd + - auto: "imglib2/*" sidebar: false format: diff --git a/bdv.qmd b/bdv/index.qmd similarity index 96% rename from bdv.qmd rename to bdv/index.qmd index 7856678..d94ab97 100644 --- a/bdv.qmd +++ b/bdv/index.qmd @@ -1,6 +1,6 @@ --- title: "BigDataViewer" -image: logos/bdv.png +image: ../logos/bdv.png about: template: solana links: @@ -10,6 +10,7 @@ about: format: html: code-tools: false +sidebar: true --- The BigDataViewer is a re-slicing browser for terabyte-sized multi-view image sequences. diff --git a/imglib2/index.md b/imglib2/index.md deleted file mode 100644 index 84dbc96..0000000 --- a/imglib2/index.md +++ /dev/null @@ -1,56 +0,0 @@ ---- -title: ImgLib2 - -doi: 10.1093/bioinformatics/bts543 -project-blurb: the ImgLib2 multidimensional image processing library -sidebar: true - ---- - -ImgLib2 is a general-purpose, multidimensional image processing library. - -It provides an interface-driven design that supports numeric and non-numeric data types (8-bit unsigned integer, 32-bit floating point, etc.) in an extensible way. It implements several data sources and sample organizations, including one single primitive array, one array per plane, N-dimensional array "cells" cached to and from disk on demand, and planes read on demand from disk. - -## Resources - -- [ImgLib2 paper](http://bioinformatics.oxfordjournals.org/content/28/22/3009.full) -- [ImgLib2 Documentation](/libs/imglib2/documentation) -- [ImgLib2 Examples](/libs/imglib2/examples) -- [ImgLib2 Blog](https://imglib.github.io/imglib2-blog/) -- [Image.sc forum](https://forum.image.sc/tag/imglib2) -- {% include javadoc project='ImgLib2' %} javadoc -- [How To Migrate Code From ImgLib To ImgLib2](/libs/imglib2/migrate-from-imglib1) -- ["Introduction to ImgLib2"](/libs/imglib2/workshop-introductory) workshop -- ["Advanced Programming with ImgLib2"](/libs/imglib2/workshop-advanced) workshop -- ["I2K 2020 Introductory ImgLib2"](https://github.com/saalfeldlab/i2k2020-imglib2-intro) workshop -- ["I2K 2020 Advanced ImgLib2"](https://github.com/saalfeldlab/i2k2020-imglib2-advanced) workshop - -## Source code - -You can find the source {% include github org='imglib' repo='imglib2' %}. - -There is also a [continuous integration](/develop/ci) system that builds ImgLib2 [every time the code changes](https://github.com/imglib/imglib2/actions). - -## ImgLib2 vs. ImgLib1 - -[ImgLib1](/libs/imglib1) is the previous incarnation of the library. We encourage developers to use ImgLib2 instead, and [migrate existing ImgLib1 programs to ImgLib2](/libs/imglib2/migrate-from-imglib1) whenever possible. - -For an explanation of how ImgLib2 has changed from ImgLib1, see the [Changes from ImgLib1 to ImgLib2](/libs/imglib2/changes-from-imglib1) page. - -See the [How To Migrate Code From ImgLib To ImgLib2](/libs/imglib2/migrate-from-imglib1) page for details on how to update your ImgLib1-based code to use ImgLib2. - -## API Version History - -A history of API changes is available at: [https://abi-laboratory.pro/java/tracker/timeline/imglib2/](https://abi-laboratory.pro/java/tracker/timeline/imglib2/) - -## Other links - -- [ImgLib2 development discussion](/libs/imglib2/discussion) -- [ImgLib2 performance benchmarks](/libs/imglib2/benchmarks) -- [ImageJ2](/software/imagej2) uses ImgLib2 as its core data model - -## Publication - -Pietzsch, T., Preibisch, S., Tomančák, P., & Saalfeld, S. (2012). [ImgLib2—generic image processing in Java](http://bioinformatics.oxfordjournals.org/content/28/22/3009.full). Bioinformatics, 28(22), 3009-3011. - - diff --git a/imglib2.qmd b/imglib2/index.qmd similarity index 55% rename from imglib2.qmd rename to imglib2/index.qmd index 53e62df..885f1ed 100644 --- a/imglib2.qmd +++ b/imglib2/index.qmd @@ -1,6 +1,6 @@ --- title: "ImgLib2" -image: logos/imglib2.png +image: ../logos/imglib2.png sidebar: true format: html: @@ -15,7 +15,6 @@ about: - icon: github text: Github href: https://github.com/imglib - --- ImgLib2 is a general-purpose, multidimensional image and data processing library. @@ -75,3 +74,45 @@ BdvFunctions.show( BdvOptions.options().is2D()).setDisplayRange(0, 64); ``` +## Resources + +- [ImgLib2 paper](http://bioinformatics.oxfordjournals.org/content/28/22/3009.full) +- [ImgLib2 Documentation](/libs/imglib2/documentation) +- [ImgLib2 Examples](/libs/imglib2/examples) +- [ImgLib2 Blog](https://imglib.github.io/imglib2-blog/) +- [Image.sc forum](https://forum.image.sc/tag/imglib2) +- {% include javadoc project='ImgLib2' %} javadoc +- [How To Migrate Code From ImgLib To ImgLib2](/libs/imglib2/migrate-from-imglib1) +- ["Introduction to ImgLib2"](/libs/imglib2/workshop-introductory) workshop +- ["Advanced Programming with ImgLib2"](/libs/imglib2/workshop-advanced) workshop +- ["I2K 2020 Introductory ImgLib2"](https://github.com/saalfeldlab/i2k2020-imglib2-intro) workshop +- ["I2K 2020 Advanced ImgLib2"](https://github.com/saalfeldlab/i2k2020-imglib2-advanced) workshop + +## Source code + +You can find the source {% include github org='imglib' repo='imglib2' %}. + +There is also a [continuous integration](/develop/ci) system that builds ImgLib2 [every time the code changes](https://github.com/imglib/imglib2/actions). + +## ImgLib2 vs. ImgLib1 + +[ImgLib1](/libs/imglib1) is the previous incarnation of the library. We encourage developers to use ImgLib2 instead, and [migrate existing ImgLib1 programs to ImgLib2](/libs/imglib2/migrate-from-imglib1) whenever possible. + +For an explanation of how ImgLib2 has changed from ImgLib1, see the [Changes from ImgLib1 to ImgLib2](/libs/imglib2/changes-from-imglib1) page. + +See the [How To Migrate Code From ImgLib To ImgLib2](/libs/imglib2/migrate-from-imglib1) page for details on how to update your ImgLib1-based code to use ImgLib2. + +## API Version History + +A history of API changes is available at: [https://abi-laboratory.pro/java/tracker/timeline/imglib2/](https://abi-laboratory.pro/java/tracker/timeline/imglib2/) + +## Other links + +- [ImgLib2 development discussion](/libs/imglib2/discussion) +- [ImgLib2 performance benchmarks](/libs/imglib2/benchmarks) +- [ImageJ2](/software/imagej2) uses ImgLib2 as its core data model + +## Publication + +Pietzsch, T., Preibisch, S., Tomančák, P., & Saalfeld, S. (2012). [ImgLib2—generic image processing in Java](http://bioinformatics.oxfordjournals.org/content/28/22/3009.full). Bioinformatics, 28(22), 3009-3011. + diff --git a/index.qmd b/index.qmd index ab90694..1e99136 100644 --- a/index.qmd +++ b/index.qmd @@ -21,8 +21,8 @@ format: sidebar: false --- -[![](logos/imglib2.png)](imglib2.qmd){fig-align="left" width=40% height=40%} -[![](logos/bdv.png)](bdv.qmd){fig-align="right" width=40% height=40%} +[![](logos/imglib2.png)](imglib2){fig-align="left" width=40% height=40%} +[![](logos/bdv.png)](bdv){fig-align="right" width=40% height=40%}