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* 'master' of github.com:scalableminds/webknossos:
  [Docs] Update embedded YouTube URLs (#7102)
  Show organization in dataset info tab (#7087)
  Added Tutorials to Docs (#7095)
  Combine both download modals into one (#7068)
  Add "merge" blend mode (#6936)
  Changed the spacing/width of VX reports runs selection (#7094)
  Allow dataset managers to see all workflow reports of their orga (#7081)
  Fix rectangle at 0,0,0 (#7088)
  Allow to disable automatic reloading of meshes during proofreading (#7076)
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hotzenklotz committed May 30, 2023
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7 changes: 7 additions & 0 deletions CHANGELOG.unreleased.md
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Expand Up @@ -12,19 +12,25 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released

### Added
- Added segment groups so that segments can be organized in a hierarchy (similar to skeletons). [#6966](https://github.com/scalableminds/webknossos/pull/6966)
- Added a new "cover" blend mode which renders the visible layers on top of each other. The new blend mode can be selected in the Data Rendering settings in the settings tab of the left side bar. [#6936](https://github.com/scalableminds/webknossos/pull/6936)
- In addition to drag and drop, the selected tree(s) in the Skeleton tab can also be moved into another group by right-clicking the target group and selecting "Move selected tree(s) here". [#7005](https://github.com/scalableminds/webknossos/pull/7005)
- Added a machine-learning based quick select mode. Activate it via the "AI" button in the toolbar after selecting the quick-select tool. [#7051](https://github.com/scalableminds/webknossos/pull/7051)
- Added support for remote datasets encoded with [brotli](https://datatracker.ietf.org/doc/html/rfc7932). [#7041](https://github.com/scalableminds/webknossos/pull/7041)
- Teams can be edited more straight-forwardly in a popup in the team edit page. [#7043](https://github.com/scalableminds/webknossos/pull/7043)
- Added support to download layers of a dataset as (OME) TIFF files in the download modal when viewing a dataset. [#7068](https://github.com/scalableminds/webknossos/pull/7068)
- Annotations with Editable Mappings (a.k.a Supervoxel Proofreading) can now be merged. [#7026](https://github.com/scalableminds/webknossos/pull/7026)
- The file size and inodes of artifacts are now aggregated and shown in the Voxelytics workflow list. [#7071](https://github.com/scalableminds/webknossos/pull/7071)
- It is possible to disable the automatic loading of meshes during proofreading. [##7076](https://github.com/scalableminds/webknossos/pull/7076)
- When viewing a public dataset by another organization, the organization is shown next to the dataset list, and when viewing the dataself or an annotation. [#7087](https://github.com/scalableminds/webknossos/pull/7087)
- Added new graphics and restyled empty dashboards. [#7008](https://github.com/scalableminds/webknossos/pull/7008)

### Changed
- Loading of precomputed meshes got significantly faster (especially when using a mesh file for an oversegmentation with an applied agglomerate mapping). [#7001](https://github.com/scalableminds/webknossos/pull/7001)
- Improved speed of proofreading by only reloading affected areas after a split or merge. [#7050](https://github.com/scalableminds/webknossos/pull/7050)
- The minimum length of layer names in datasets was set from 3 to 1, enabling single-character names for layers. [#7064](https://github.com/scalableminds/webknossos/pull/7064)
- All dataset managers are now allowed to see all voxelytics workflow reports created in their organization. Previously, only admins could see all workflow reports, with other users seeing only their own. [#7080](https://github.com/scalableminds/webknossos/pull/7080)
- Improved performance for large meshes, especially when loaded from a precomputed oversegmentation mesh file. [#7077](https://github.com/scalableminds/webknossos/pull/7077)
- Slight increased the spacing and width of some VX reports elements. [#7094](https://github.com/scalableminds/webknossos/pull/7094)

### Fixed
- Fixed that changing a segment color could lead to a crash. [#7000](https://github.com/scalableminds/webknossos/pull/7000)
Expand All @@ -46,6 +52,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
- Fixed displayed units of used storage in the organization's overview page. [#7057](https://github.com/scalableminds/webknossos/pull/7057)
- Fixed a rendering bug that could occur when a dataset layer has missing mags (e.g., the first mag is 8-8-8). [#7082](https://github.com/scalableminds/webknossos/pull/7082)
- Fixed a bug where some volume annotations could not be duplicated or used as tasks. [#7085](https://github.com/scalableminds/webknossos/pull/7085)
- Fixed a superfluous rectangular geometry rendered at 0,0,0. [#7088](https://github.com/scalableminds/webknossos/pull/7088)

### Removed

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2 changes: 1 addition & 1 deletion app/models/voxelytics/VoxelyticsDAO.scala
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Expand Up @@ -51,7 +51,7 @@ class VoxelyticsDAO @Inject()(sqlClient: SqlClient)(implicit ec: ExecutionContex
private def visibleRunsQ(currentUser: User, allowUnlisted: Boolean) = {
val organizationId = currentUser._organization
val readAccessQ =
if (currentUser.isAdmin || allowUnlisted) q"${true}"
if (currentUser.isAdmin || currentUser.isDatasetManager || allowUnlisted) q"${true}"
else q"(__r._user = ${currentUser._id})"
q"""SELECT __r.*
FROM webknossos.voxelytics_runs __r
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13 changes: 7 additions & 6 deletions docs/dashboard.md
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Expand Up @@ -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).

Expand All @@ -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)
![youtube-video](https://www.youtube.com/embed/naPL1jfCdOc)

## Tasks

Expand All @@ -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.
Expand All @@ -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)

60 changes: 31 additions & 29 deletions docs/getting_started.md
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Expand Up @@ -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)
![youtube-video](https://www.youtube.com/embed/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.

Expand All @@ -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).
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