scalableminds · hotzenklotz · Sep 19, 2025 · Sep 17, 2025 · Sep 17, 2025 · Sep 18, 2025
diff --git a/docs/automation/animations.md b/docs/automation/animations.md
@@ -8,17 +8,40 @@ A picture is worth a thousand words. In this spirit, you can use WEBKNOSSOS to c
 
 Creating an animation is easy:
 
-1. Open any dataset or annotation that you want to use for your animation. 
+1. Open any dataset or annotation that you want to use for your animation.
 2. Optionally, load some [3D meshes](../meshes/index.md) for any segments that you wish to highlight.
 3. For larger datasets, use the bounding box tool to create a bounding box around your area of interest. Smaller datasets can be used in their entirety.
-4. From the `Menu` dropdown in navbar at the top of the screen, select "Create Animation".
-5. Configure the animation options as desired, i.e. camera movement and positioning or video resolution.
-6. Click the `Start animation` button to launch the animation creation.
-
+4. From the `Menu` dropdown in the navbar at the top of the screen, select "Create Animation".
+5. Configure the animation options in the modal that opens.
+6. Click the `Start Animation` button to launch the animation creation.
 
 Either periodically check the [background jobs page](./jobs.md) or wait for an email confirmation to download the animation video file. Creating an animation may take a while, depending on the selected bounding box size and the number of included 3D meshes.
 
-WEBKNOSSOS Team plans and above have access to high definition (HD) resolution videos and more options.
+## Animation Options
+
+The "Create Animation" modal offers several options to customize your animation:
+
+### Camera Position
+
+This setting determines the movement of the camera in the animation.
+
+- **Camera circling around the dataset:** The camera will rotate around the center of the bounding box.
+- **Static camera looking at XY/XZ/YZ-viewport:** The camera will be fixed on one of the 2D viewports.
+- **Static camera with an isometric perspective:** The camera will be in a fixed position showing a 3D view of the data.
+
+### Movie Resolution
+
+You can choose between two resolutions for your animation video:
+
+- **Standard Definition (640x360):** A smaller resolution, suitable for quick previews or sharing.
+- **High Definition (1920x1080):** A full HD resolution, ideal for presentations and high-quality showcases. Access to this option may depend on your WEBKNOSSOS plan.
+
+### Options
+
+- **Include the currently selected 3D meshes:** If checked, the animation will include any meshes that are currently loaded in the 3D view.
+- **Include WEBKNOSSOS Watermark:** If checked, the WEBKNOSSOS logo will be displayed as a watermark on the animation video. Access to this option may depend on your WEBKNOSSOS plan.
 
-![youtube-video](https://www.youtube.com/embed/4J3zQgqolAk)
+### Layer & Bounding Box
 
+- **Layer:** Select the data layer to be used for the animation.
+- **Bounding Box:** Choose the bounding box for the animation. By default, the entire layer is selected. You can create custom bounding boxes using the [bounding box tool](../ui/toolbar.md#measurement-tools).
diff --git a/docs/dashboard/datasets.md b/docs/dashboard/datasets.md
@@ -11,6 +11,4 @@ If you are [an Admin, a Dataset Manager or a Team Manager](../users/access_right
 
 Read more about the organization of datasets [here](../datasets/organization.md).
 
-![Dashboard for Team Managers or Admins with access to dataset settings and additional administration actions.](../images/screenshot_DS_management.png)
-
-![Dashboard for Regular Users](../images/dashboard_regular_user.jpeg)
+![Dashboard for Team Managers or Admins with access to dataset settings and additional administration actions.](../images/screenshot_DS_management.png)
diff --git a/docs/datasets/settings.md b/docs/datasets/settings.md
@@ -1,76 +1,84 @@
-#  Dataset Settings
-You can configure the metadata, permission, and other properties of a dataset at any time. 
+# Dataset Settings
 
-Note, any changes made to a dataset may influence the user experience of all users in your organization working with that dataset, e.g., removing access rights working, adding/removing layers, or setting default values for rendering the data.
+You can configure the metadata, permission, and other properties of a dataset at any time. To make changes, click on the **Settings** action next to a dataset in the **Datasets** tab of your dashboard.
 
-To make changes, click on the "Settings" action next to a dataset in the "Datasets" tab of your dashboard.
-Editing these settings requires your account to have enough access rights and permissions. [Read more about this.](../users/access_rights.md)
+Note that any changes made to a dataset may influence the user experience of all users in your organization working with that dataset, e.g., removing access rights, adding/removing layers, or setting default values for rendering the data.
 
-## Data Tab
-The *Data* tab contains the settings for correctly reading the dataset as the correct data type (e.g., `uint8`), setting up, and configuring any layers.
+Editing these settings requires your account to have sufficient access rights and permissions. [Read more about this.](../users/access_rights.md)
 
-- `Name`: The name of the dataset. Datasets can have duplicate names even within the same organization.
-- `Voxel Size`: The physical size of a voxel in the configured unit, e.g., `11, 11, 24`
-- `Unit`: The unit of the voxel size.
+## Data Source Tab
 
-For each detected layer:
+The `Data Source` tab contains the core settings for your dataset.
 
-- `Bounding Box`: The position and extents of the dataset layer in voxel coordinates. The format is `x, y, z, x_size,y_size, z_size` or respectively `min_x, min_y, min_z, (max_x - min_x), (max_y - min_y), (max_z - min_z)`.
-- `Largest Segment ID`: The highest ID that is currently used in a segmentation layer. When a user wants to annotate a new segment and clicks "Create new Segment Id" in the toolbar, the new ID is generated by incrementing the currently known largest segment id. This value is stored per annotation and is based on the corresponding property of the underlying dataset layer. If the id is not known, the user cannot generate new segment ids. However, they can still change the currently active ID to arbitrary values. Also, they can enter a largest segment id for their annotation without having to edit the dataset's value here (which they might not have the permissions for).
+### General Dataset Settings
 
-The `Advanced` view lets you edit the underlying [JSON configuration](../data/concepts.md#dataset-metadata) directly. Toggle between the `Advanced` and `Simple` page in the upper right. Advanced mode is only recommended for low-level access to dataset properties and users familiar with the `datasource-properties.json` format.
+- **Name:** The name of the dataset. This is also the display name that will be shown in the UI.
+- **Dataset ID:** A unique identifier for the dataset (read-only).
+- **Voxel Size:** The physical size of a voxel in the configured unit (e.g., `11, 11, 24`).
+- **Unit:** The unit of the voxel size (e.g., `nm`).
 
-WEBKNOSSOS automatically periodically checks and detects changes to a dataset's metadata (`datasource-properties.json`) on disk (only relevant for self-hosted instances). Before applying these suggestions, users can preview all the new settings (as JSON) and inspect just the detected difference (as JSON).
+### Axis Rotation
 
-![Dataset Editing: Data Tab](../images/dataset_data.jpeg)
+You can rotate the dataset around the X, Y, and Z axes. You can also mirror the axes.
+
+### Layer Settings
+
+For each layer in the dataset, you can configure:
+
+- **Name:** The name of the layer.
+- **Bounding Box:** The position and extents of the layer in voxel coordinates. The format is `x, y, z, x_size,y_size, z_size` or respectively `min_x, min_y, min_z, (max_x - min_x), (max_y - min_y), (max_z - min_z)`.
+- **Category:** The type of the layer, i.e.  `color` for raw microscopy data and `segmentation` for segmentations.
+- **Largest Segment ID**: (Segmentation layer only). The highest ID that is currently used in a segmentation layer. When a user wants to annotate a new segment and clicks "Create new Segment Id" in the toolbar, the new ID is generated by incrementing the currently known largest segment id. This value is stored per annotation and is based on the corresponding property of the underlying dataset layer. If the id is not known, the user cannot generate new segment ids. However, they can still change the currently active ID to arbitrary values. Also, they can enter a largest segment id for their annotation without having to edit the dataset's value here (which they might not have the permissions for).!
+
+![Dataset Editing: Data Source Tab](../images/dataset_settings_datasource.jpeg)
+
+
+### Advanced View
+
+The `Advanced` view lets you edit the underlying [JSON configuration](../data/concepts.md#dataset-metadata) directly. This is only recommended for users familiar with the `datasource-properties.json` format.
 
 
 ## Sharing & Permissions Tab
-- `Make dataset publicly accessible`: By default, a dataset can only be accessed by users from your organization with the correct access permissions. Turning a dataset to *public* will allow anyone in the general public to view the dataset when sharing a link to the dataset without the need for a WEBKNOSSOS account. Anyone can start using this dataset to create annotations. Enable this setting if you want to share a dataset in a publication, social media, or any other public website.
-- `Teams allowed to access this dataset`: Defines which [teams of your organization](../users/teams.md) have permission to work with this dataset. By default, no team has access, but users with *admin* and *team manager* roles can see and edit the dataset.
-- `Sharing Link`: A web URL pointing to this dataset for easy sharing that allows any user to view your dataset. The URL contains an access token to allow people to view the dataset without a WEBKNOSSOS account. The access token is random, and therefore the URL cannot be guessed by visitors. You may also revoke the access token to create a new one. Anyone with a URL containing a revoked token will no longer have access to this dataset. 
-Read more in [the Sharing guide](../sharing/dataset_sharing.md).
 
-![Dataset Editing: Sharing Tab](../images/sharing_tab.jpeg)
+This tab allows you to control who can access your dataset.
 
-## Metadata Tab
-- `Display Name`: A meaningful name for a dataset other than its (automatically assigned) technical name which is usually limited by the naming rules of file systems. It is displayed in various parts of WEBKNOSSOS. The display name may contain special characters and can also be changed without invalidating already created sharing URLs. It can also be useful when sharing datasets with outsiders while "hiding" any internal naming schemes or making it more approachable, e.g., `L. Simpson et al.: Full Neuron Segmentation` instead of `neuron_seg_v4_2022`.
-- `Description`: A free-text field for providing more information about your datasets, e.g., authors, paper reference, descriptions, etc. Supports Markdown formatting. The description will be featured in the WEBKNOSSOS UI when opening a dataset in view mode.
+- **Make dataset publicly accessible:** By default, a dataset can only be accessed by users from your organization with the correct access permissions. Turning a dataset to *public* will allow anyone to view the dataset with a sharing link, without needing a WEBKNOSSOS account.
+- **Additional team access permissions for this dataset:** Defines which [teams of your organization](../users/teams.md) have permission to work with this dataset.
+- **Sharing Link:** A URL to share the dataset with others. You can renew the access token to invalidate the old link.
+- **Users with access permission to work with this dataset:** A list of all users that have access to the dataset.
 
-![Dataset Editing: Metadata Tab](../images/metadata_tab.jpeg)
+Read more in [the Sharing guide](../sharing/dataset_sharing.md).
 
-## View Configuration Tab
-The *View configuration* tab lets you set defaults for viewing this dataset. Anytime a user opens a dataset or creates a new annotation based on this dataset, these default values will be applied. 
+![Dataset Editing: Sharing Tab](../images/dataset_settings_sharing.jpeg)
 
-Defaults include:
 
-- `Position`: Default position of the dataset in voxel coordinates. When opening the dataset, users will be located at this position.
-- `Zoom`: Default zoom.
-- `Interpolation`: Whether interpolation should be enabled by default.
-- `Layer Configuration`: Advanced feature to control the default settings on a per-layer basis. It needs to be configured in JSON format. E.g., layer visibility & opacity, color, contrast/brightness/intensity range ("histogram sliders"), and many more.
+## Metadata Tab
 
-![Dataset Editing: View Configuration Tab](../images/dataset_view_config.jpeg)
+This tab allows you to add descriptive information to your dataset.
 
-Alternatively, these settings can be configured in a more intuitive way by opening the dataset in view mode. Change the current view settings to the desired result and save them as the dataset's default using the "Save View Configuration as Default" button in the layer settings tab.
+- **Publication Date:** The date the dataset was published. This influences the dataset ordering in your dashboard.
+- **Description:** A free-text field for providing more information about your dataset, such as authors, paper references, etc. It supports Markdown formatting.
 
-![Saving the view configuration in view mode](../images/save_view_configuration_in_view_mode.png)
+![Dataset Editing: Metadata Tab](../images/dataset_settings_metadata.jpeg)
+
+
+## View Configuration Tab
 
-Of course, the defaults can all be overwritten and adjusted once a user opens the dataset in the main WEBKNOSSOS interface and makes changes to any of these settings in his viewports. 
+The `View Configuration` tab lets you set the default viewing parameters for this dataset. These defaults will be applied whenever a user opens the dataset for the first time.
 
-For self-hosted WEBKNOSSOS instances, there are three ways to set default *View Configuration* settings:
+- **Position, Zoom, and Rotation:** Set the default camera position, zoom level, and rotation.
+- **Rendering Options:** Configure default rendering settings like `Interpolation`, `4 Bit` rendering, and `Blend Mode`.
+- **Layer Configuration:** An advanced feature to control the default settings on a per-layer basis using a JSON object. You can configure properties like visibility, opacity, color, and intensity range.
 
-- in the web UI as described above
-- while viewing the dataset
-- inside the `datasource_properties.json` on disk
+Alternatively, you can set the default view configuration from the main annotation view by clicking the "Save View Configuration as Default" button in the layer settings.
 
-The *View Configuration* from the web UI takes precedence over the `datasource_properties.json`.
-You don't have to set complete *View Configurations* in either option, as WEBKNOSSOS will fill missing attributes with sensible defaults.
+![Dataset Editing: View Configuration Tab](../images/dataset_settings_viewconfig.jpeg)
 
 
 ## Delete Tab
 
-Offers an option to delete a dataset and completely remove it from WEBKNOSSOS. Be careful, this cannot be undone!
+This tab offers an option to delete the dataset. This action is irreversible and will permanently remove the dataset from WEBKNOSSOS.
 
-When other datasets reference layers from this dataset, WEBKNOSSOS will try to move these layers to the dataset they are referenced in, so that it can still be accessed.
+Deleting an dataset will not delete any annotations associated with it.
 
-![Dataset Editing: Delete Tab](../images/delete_tab.jpeg)
+![Dataset Editing: Delete Tab](../images/dataset_settings_delete.jpeg)
diff --git a/docs/images/dataset_data.jpeg b/docs/images/dataset_data.jpeg
diff --git a/docs/images/dataset_general.jpeg b/docs/images/dataset_general.jpeg
diff --git a/docs/images/dataset_settings_datasource.jpeg b/docs/images/dataset_settings_datasource.jpeg
diff --git a/docs/images/dataset_settings_delete.jpeg b/docs/images/dataset_settings_delete.jpeg
diff --git a/docs/images/dataset_settings_metadata.jpeg b/docs/images/dataset_settings_metadata.jpeg
diff --git a/docs/images/dataset_settings_sharing.jpeg b/docs/images/dataset_settings_sharing.jpeg
diff --git a/docs/images/dataset_settings_viewconfig.jpeg b/docs/images/dataset_settings_viewconfig.jpeg
diff --git a/docs/images/dataset_view_config.jpeg b/docs/images/dataset_view_config.jpeg
diff --git a/docs/images/delete_tab.jpeg b/docs/images/delete_tab.jpeg
diff --git a/docs/images/metadata_tab.jpeg b/docs/images/metadata_tab.jpeg
diff --git a/docs/images/sharing_tab.jpeg b/docs/images/sharing_tab.jpeg
diff --git a/docs/sharing/dataset_sharing.md b/docs/sharing/dataset_sharing.md
@@ -33,8 +33,9 @@ To share a dataset privately, follow these steps:
 
 To revoke a sharing link in the future, click the `Revoke` button on the right-hand side of the link.
 
-**Do not enable the `Make dataset publicly accessible` checkbox otherwise, anyone with a link can access this dataset without needing to log in/authenticate.
-Public access rights are not required for private sharing.**
+!!!warning
+    Do not enable the `Make dataset publicly accessible` checkbox otherwise, anyone with a link can access this dataset without needing to log in/authenticate.
+    Public access rights are not required for private sharing.
 
 ## Public Sharing
 
@@ -56,5 +57,6 @@ To share a dataset publicly, follow these steps:
 
 ![The Metadata tab overview](../images/metadata_tab.jpeg)
 
-**We recommend giving your datasets a meaningful display name and description. Both are featured next to the data viewport in the `Info` tab in the main WEBKNOSSOS UI.**
+!!!info
+    We recommend giving your datasets a meaningful name and description. Both are featured next to the data viewport in the `Info` tab in the main WEBKNOSSOS UI.
 
diff --git a/docs/today_i_learned.md b/docs/today_i_learned.md
@@ -2,9 +2,12 @@
 
 We regularly publish tips and tricks videos for beginners and pros on YouTube to share new features, highlight efficient workflows, and show you hidden gems.
 
+Subscribe to our YouTube channel [@webknossos](https://www.youtube.com/@webknossos) or [@webknossos.org](https://bsky.app/profile/webknossos.org) on Bluesky to stay up-to-date. 
+
+Please enjoy this playlist of our latest tips and tricks:
+
 <figure class="video_container">
   <iframe width="560" height="560" src="https://www.youtube-nocookie.com/embed/videoseries?si=CqXiVKkxxFU8uETH&amp;list=PLpizOgyiA4kEGKFRQFOgjucZCKtI2GUZY&autoplay=1&loop=1&mute=1" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
 </figure>
 
-Subscribe to our YouTube channel [@webknossos](https://www.youtube.com/@webknossos) or [@webknossos.org](https://bsky.app/profile/webknossos.org) on Bluesky to stay up-to-date.