scalableminds · hotzenklotz · May 25, 2023 · May 23, 2023 · May 23, 2023 · May 23, 2023
diff --git a/docs/dashboard.md b/docs/dashboard.md
@@ -4,8 +4,9 @@ The Dashboard is your entry point to WEBKNOSSOS.
 You can manage your datasets, create annotations, resume existing annotations and retrieve tasks distributed to you.
 
 ## Datasets
+
 This screen shows all the available and accessible datasets for a user.
-You can *view* a dataset (read-only) or start new annotations from this screen.
+You can _view_ a dataset (read-only) or start new annotations from this screen.
 Search for your dataset by using the search bar or sorting any of the table columns.
 Learn more about managing datasets in the [Datasets guide](./datasets.md).
 
@@ -18,7 +19,7 @@ Read more about the organization of datasets [here](./datasets.md#dataset-organi
 ![Dashboard for Team Managers or Admins with access to dataset settings and additional administration actions.](./images/dashboard_datasets.jpeg)
 ![Dashboard for Regular Users](./images/dashboard_regular_user.jpeg)
 
-![Video: Community Dataset Gallery & Navigating Through Data](https://www.youtube.com/watch?v=naPL1jfCdOc)
+![type:video](https://www.youtube.com/watch?v=naPL1jfCdOc)
 
 ## Tasks
 
@@ -31,17 +32,18 @@ Read more about the tasks feature in the [Tasks and Projects guide](./tasks.md).
 ![Tasks can be distributed to users. Task can include rich instructions.](./images/dashboard_tasks.jpeg)
 
 ## Annotations
+
 This screen lists all your annotations (skeleton, volume or both) that you started on a dataset (outside of tasks) and annotations that were shared with you. Annotations are either created by starting new annotations from the "Datasets" tab, from the WEBKNOSSOS data viewer, or by uploading an existing annotation from your computer (see [NML files](./data_formats.md#nml) for skeleton annotations).
 
-Annotations can be resumed, archived (like delete, but reversible), and downloaded for offline analysis. 
-You can also add custom tags to annotations to organize and group them. Click on one or multiple of your tags if you want to filter a particular group of annotations. 
+Annotations can be resumed, archived (like delete, but reversible), and downloaded for offline analysis.
+You can also add custom tags to annotations to organize and group them. Click on one or multiple of your tags if you want to filter a particular group of annotations.
 Each annotation can be renamed to reflect its content.
 
 ![Manage and resume your skeleton and volume annotations.](./images/dashboard_annotations.jpeg)
 ![Annotations can archived to declutter your dashboard.](./images/dashboard_archive.jpeg)
 
-
 ### Sharing Annotations
+
 The annotations tab also shows all annotations that were shared by other collaborators of your organization. Only annotations shared through the "Team Sharing" mechanic will be listed provided your user account is part of the respective team. Read more about sharing your own annotations in the [Sharing guide](./sharing.md#annotation-sharing).
 
 You can view the linked annotations (read-only) or copy them to your account for modification.
@@ -53,4 +55,3 @@ This screen lists a number of featured public community datasets and their respe
 [Contact us](mailto:[email protected]) if you would like your data and publication to be featured here as well.
 
 ![The list of featured community datasets.](./images/dashboard_featured_publications.jpeg)
-
diff --git a/docs/getting_started.md b/docs/getting_started.md
@@ -6,9 +6,10 @@ Since it is a web-based tool, [collaboration](./sharing.md), [crowdsourcing](./t
 
 Feel free to [contact us](mailto:[email protected]) or [create a Pull Request](https://github.com/scalableminds/webknossos/pulls) if you have any suggestions for improving the documentation.
 
-![Video: Beginner's Guide](https://www.youtube.com/watch?v=jsz0tc3tuKI)
+![type:video](https://www.youtube.com/watch?v=jsz0tc3tuKI)
 
 ## Create a webknossos.org Account
+
 Signing up for a free account on [webknossos.org](https://webknossos.org) is the easiest and fastest way to get started with WEBKNOSSOS.
 Either upload one of your own datasets and explore one of the many community datasets.
 
@@ -18,71 +19,72 @@ For more data storage, check out the [pricing page for paid plans](https://webkn
 If you are looking for on-premise hosting at your institute or custom solutions, [please reach out to us](mailto:[email protected]).
 
 ## Explore Published Datasets
+
 [webknossos.org](https://webknossos.org) comes with a large number of published community datasets available for you to explore.
 To get started, navigate to the `Featured Publications` tab on your [dashboard](./dashboard.md).
 There, you find a list of all available public datasets.
 Click on the dataset name to open the dataset.
 
 ![The list of available datasets](./images/getting_started-datasets.jpeg)
 
-Any WEBKNOSSOS dataset can be opened for read-only viewing ("View" mode) or in editor-mode to create a new skeleton and/or volume annotation. 
+Any WEBKNOSSOS dataset can be opened for read-only viewing ("View" mode) or in editor-mode to create a new skeleton and/or volume annotation.
 The main WEBKNOSSOS user interface consists of three orthogonal viewports slicing the data along the major axis and a 3D viewport. Read more about the UI in the section [about the UI](./tracing_ui.md).
 
 ![The WEBKNOSSOS user interface consisting of three orthogonal viewports slicing the data along the major axis and a 3D viewport.](./images/main_ui.jpeg)
 
 You can use the following shortcuts to navigate the data.
 See the full list of [gestures and keyboard shortcuts](./keyboard_shortcuts.md) for advanced use.
 
-| Shortcut                      | Operation                       |
-| ----------------------------- | ------------------------------- |
-| Left Mouse Drag or Arrow Keys | Move In-Plane                   |
-| SPACE or Mousewheel           | Move Forward                    |
-| SHIFT + SPACE or Mousewheel   | Move Backward                   |
-| I or ALT + Mousewheel         | Zoom In                         |
-| O or ALT + Mousewheel         | Zoom Out                        |
-| Scroll Mousewheel (3D View)   | Zoom In And Out                 |
-| Right Click Drag (3D View)    | Rotate 3D View                  |
-| . (Dot)                       | Toggle Viewport Maximization    |
+| Shortcut                      | Operation                    |
+| ----------------------------- | ---------------------------- |
+| Left Mouse Drag or Arrow Keys | Move In-Plane                |
+| SPACE or Mousewheel           | Move Forward                 |
+| SHIFT + SPACE or Mousewheel   | Move Backward                |
+| I or ALT + Mousewheel         | Zoom In                      |
+| O or ALT + Mousewheel         | Zoom Out                     |
+| Scroll Mousewheel (3D View)   | Zoom In And Out              |
+| Right Click Drag (3D View)    | Rotate 3D View               |
+| . (Dot)                       | Toggle Viewport Maximization |
 
 You can also change the size of the viewports to see more details in your data and customize your layout.
 
 ![Explore datasets with customized viewport layouts](./images/getting_started-viewports.jpeg)
 
-
 ## Your First Annotation
+
 Click the `Create Annotation` button while in "View" mode to create your first annotation.
 WEBKNOSSOS will launch the main annotation screen allowing you to navigate your dataset, place markers to reconstruct skeletons, or annotate segments as volume annotations.
 
 Depending on the current tool - selectable in the top bar - various actions can be performed.
 Note that the most important controls are always shown in the status bar at the bottom of your screen.
-The first tool is the *Move* tool which allows navigating the dataset by moving the mouse while holding the left mouse button.
-With the *SKeleton* tool, a left mouse click can be used to place markers in the data, called nodes.
+The first tool is the _Move_ tool which allows navigating the dataset by moving the mouse while holding the left mouse button.
+With the _SKeleton_ tool, a left mouse click can be used to place markers in the data, called nodes.
 Additionally, the left mouse button can also be used to navigate around, select or drag nodes.
-The *Brush* and *Trace* tools allow to "paint" voxels to create volumetric annotations. 
-For a full rundown on the other annotations tools, such as *Eraser*, *Segment Picker*, *Fill* please refer to documentation on [skeleton](./skeleton_annotation.md) and [volume](./volume_annotation.md) annotations.
+The _Brush_ and _Trace_ tools allow to "paint" voxels to create volumetric annotations.
+For a full rundown on the other annotations tools, such as _Eraser_, _Segment Picker_, _Fill_ please refer to documentation on [skeleton](./skeleton_annotation.md) and [volume](./volume_annotation.md) annotations.
 
-A right mouse click can be used to open a context-sensitive menu with various actions, such as merging two trees or flood-filling a segment. 
+A right mouse click can be used to open a context-sensitive menu with various actions, such as merging two trees or flood-filling a segment.
 Basic movement along the 3rd axis is done with the mouse wheel or by pressing the spacebar keyboard shortcut.
 
 Learn more about the skeleton, volume, and hybrid annotations as well as the interface in the [Annotation UI guide](./tracing_ui.md).
 
 ![Editing skeleton and volume annotations in the Annotation UI](./images/tracing_ui.jpeg)
 
-
 ## Learn More
+
 Now you know the basics of WEBKNOSSOS.
 Feel free to explore more features of WEBKNOSSOS in this documentation.
 
-* [Dashboard](./dashboard.md)
-* [Skeleton Annotations](./skeleton_annotation.md)
-* [Volume Annotations & Proof-Reading](./volume_annotation.md)
-* [Keyboard Shortcuts](./keyboard_shortcuts.md)
-* [Understanding the User Interface](./tracing_ui.md)
-* [Sharing](./sharing.md)
-* [Datasets](./datasets.md) and [Data Formats](./data_formats.md)
-* [User and Permission Management](./users.md)
-* [Task and Project Management](./tasks.md)
-* [FAQ](./faq.md)
+- [Dashboard](./dashboard.md)
+- [Skeleton Annotations](./skeleton_annotation.md)
+- [Volume Annotations & Proof-Reading](./volume_annotation.md)
+- [Keyboard Shortcuts](./keyboard_shortcuts.md)
+- [Understanding the User Interface](./tracing_ui.md)
+- [Sharing](./sharing.md)
+- [Datasets](./datasets.md) and [Data Formats](./data_formats.md)
+- [User and Permission Management](./users.md)
+- [Task and Project Management](./tasks.md)
+- [FAQ](./faq.md)
 
 If you need help with WEBKNOSSOS, feel free to contact us at [[email protected]](mailto:[email protected]) or [write a post in the forum](https://forum.image.sc/tag/webknossos).
 scalable minds also offers [commercial support, managed hosting, and feature development services](https://webknossos.org/pricing).

diff --git a/docs/index.md b/docs/index.md
@@ -7,29 +7,31 @@ Powerful [user](./users.md) and [task](./tasks.md) management features automatic
 There are a lot of productivity improvements to make the human part as efficient as possible.
 WEBKNOSSOS is also a platform for [showcasing datasets](https://webknossos.org) alongside a paper publication.
 
-![Video: WEBKNOSSOS: Beginner's Guide](https://www.youtube.com/watch?v=jsz0tc3tuKI)
+![type:video](https://www.youtube.com/watch?v=jsz0tc3tuKI)
 
 ## Getting Started
-Sign up for a free account on [https://webknossos.org/](https://webknossos.org/) and either upload one of your own datasets, or work with a large selection of published community datasets. 
+
+Sign up for a free account on [https://webknossos.org/](https://webknossos.org/) and either upload one of your own datasets, or work with a large selection of published community datasets.
 
 ## Features
-* Exploration of large 3D image datasets as found in electron-microscopy, synchrotron, CT, MRI, Micro/Nano-CT
-* Fully browser-based user experience. No installation required
-* Efficient 3D data streaming for quick loading speeds
-* Creation/editing of skeleton (line-segments) and 3D volumetric annotations
-* [Innovative flight mode for fast skeleton annotation](https://www.nature.com/articles/nmeth.4331)
-* User and task management for high-throughput collaboration in the lab or crowdsourcing
-* Easy Sharing. Every dataset and annotation can be securely shared as a web link with others
-* Fine-grained access permission and and user roles for secure collaboration
-* [Standalone datastore component](https://github.com/scalableminds/webknossos/tree/master/webknossos-datastore) for flexible deployments
-* [Supported dataset formats: Zarr, WKW (Optimized), KNOSSOS cubes](./data_formats.md), [Neuroglancer Precomputed, and BossDB](https://github.com/scalableminds/webknossos-connect), and image stacks (converted on upload)
-* [Supported image formats](./data_formats.md): Grayscale, Segmentation Maps, RGB, Multi-Channel
-* [3D Mesh Visualization](./mesh_visualization.md)
-* [Integrated Synapse and Connectome Viewer](./connectome_viewer.md)
-* [Documented Python library for API access and integration in custom analysis workflows](https://docs.webknossos.org/webknossos-py/index.html)
-* [Documented frontend API for user scripting](https://webknossos.org/assets/docs/frontend-api/index.html), REST API for backend access
-* Open-source development with [automated test suite](https://circleci.com/gh/scalableminds/webknossos)
-* [Docker-based deployment](https://hub.docker.com/r/scalableminds/webknossos/) for production and development
+
+- Exploration of large 3D image datasets as found in electron-microscopy, synchrotron, CT, MRI, Micro/Nano-CT
+- Fully browser-based user experience. No installation required
+- Efficient 3D data streaming for quick loading speeds
+- Creation/editing of skeleton (line-segments) and 3D volumetric annotations
+- [Innovative flight mode for fast skeleton annotation](https://www.nature.com/articles/nmeth.4331)
+- User and task management for high-throughput collaboration in the lab or crowdsourcing
+- Easy Sharing. Every dataset and annotation can be securely shared as a web link with others
+- Fine-grained access permission and and user roles for secure collaboration
+- [Standalone datastore component](https://github.com/scalableminds/webknossos/tree/master/webknossos-datastore) for flexible deployments
+- [Supported dataset formats: Zarr, WKW (Optimized), KNOSSOS cubes](./data_formats.md), [Neuroglancer Precomputed, and BossDB](https://github.com/scalableminds/webknossos-connect), and image stacks (converted on upload)
+- [Supported image formats](./data_formats.md): Grayscale, Segmentation Maps, RGB, Multi-Channel
+- [3D Mesh Visualization](./mesh_visualization.md)
+- [Integrated Synapse and Connectome Viewer](./connectome_viewer.md)
+- [Documented Python library for API access and integration in custom analysis workflows](https://docs.webknossos.org/webknossos-py/index.html)
+- [Documented frontend API for user scripting](https://webknossos.org/assets/docs/frontend-api/index.html), REST API for backend access
+- Open-source development with [automated test suite](https://circleci.com/gh/scalableminds/webknossos)
+- [Docker-based deployment](https://hub.docker.com/r/scalableminds/webknossos/) for production and development
 
 ## Screenshots
 
@@ -42,19 +44,19 @@ Sign up for a free account on [https://webknossos.org/](https://webknossos.org/)
 ![Showcasing Datasets](./images/dashboard_featured_publications.jpeg)
 
 # Built for Science
-WEBKNOSSOS is built for scientists with support by scientists. Our goal is to make image analysis and data exploration accessible and easy to use. 
+
+WEBKNOSSOS is built for scientists with support by scientists. Our goal is to make image analysis and data exploration accessible and easy to use.
 While originally designed for the annotation of electron microscopy of neural circuits, we have seen great projects using it to analyze MRI/CT scans, fluorescences microscopy images, and synchrotron datasets.
 
 WEBKNOSSOS' impact on data annotation in neuroscience and Connectomics has been published in Nature Methods, 2017 and many other [publications](./publications.md):
 
 > Boergens, Berning, Bocklisch, Bräunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler and Helmstaedter
-webKnossos: efficient online 3D data annotation for connectomics.
-[Nature Methods (2017) DOI:10.1038/NMETH.4331.](https://www.nature.com/articles/nmeth.4331)
-
+> webKnossos: efficient online 3D data annotation for connectomics.
+> [Nature Methods (2017) DOI:10.1038/NMETH.4331.](https://www.nature.com/articles/nmeth.4331)
 
 ## Credits and Help
 
 WEBKNOSSOS is developed by [scalable minds](https://scalableminds.com) in collaboration with the [Max Planck Institute for Brain Research](https://brain.mpg.de/connectomics).
 
-If you need help with WEBKNOSSOS, feel free to contact us at [[email protected]](mailto:[email protected]) or [write a post in the community forum](https://forum.image.sc/tag/webknossos). 
+If you need help with WEBKNOSSOS, feel free to contact us at [[email protected]](mailto:[email protected]) or [write a post in the community forum](https://forum.image.sc/tag/webknossos).
 scalable minds also offers [commercial support, managed hosting, and image analysis services](https://webknossos.org/pricing).