scalableminds · bulldozer-boy · Jan 17, 2023 · Jan 12, 2023 · Jan 12, 2023 · Jan 13, 2023
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -33,4 +33,4 @@ assignees: ''
 - Operating System and version: e.g. Windows 10
 - Version of WebKnossos (Release or Commit):
 - [ ] Specific to long-running jobs (set `jobsEnabled=true` in `application.conf`)
-- [ ] Specific to webKnossos.org (set `isDemoInstance=true` in `application.conf`)
+- [ ] Specific to webknossos.org (set `isDemoInstance=true` in `application.conf`)
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -13,4 +13,4 @@ assignees: ''
 ## Context
 <!--- Why is this change / new feature important ? What are its use cases? -->
 * [ ] Specific to long-running jobs (set `jobsEnabled=true` in `application.conf`)
-* [ ] Specific to webKnossos.org (set `isDemoInstance=true` in `application.conf`)
+* [ ] Specific to webknossos.org (set `isDemoInstance=true` in `application.conf`)
diff --git a/CHANGELOG.released.md b/CHANGELOG.released.md
@@ -1,6 +1,6 @@
 # Changelog (Released)
 
-All notable user-facing changes to webknossos are documented in this file.
+All notable user-facing changes to WEBKNOSSOS are documented in this file.
 See `CHANGELOG.unreleased.md` for the changes which are not yet part of an official release.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
@@ -141,7 +141,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Added
 - Zarr-based remote dataset import now also works for public AWS S3 endpoints with no credentials. [#6421](https://github.com/scalableminds/webknossos/pull/6421)
 - Added a "clear" button to reset skeletons/meshes after successful mergers/split. [#6459](https://github.com/scalableminds/webknossos/pull/6459)
-- The proofreading tool now supports merging and splitting (via min-cut) agglomerates by rightclicking a segment (and not a node). Note that there still has to be an active node so that both partners of the operation are defined. [#6464](https://github.com/scalableminds/webknossos/pull/6464)
+- The proofreading tool now supports merging and splitting (via min-cut) agglomerates by right-clicking a segment (and not a node). Note that there still has to be an active node so that both partners of the operation are defined. [#6464](https://github.com/scalableminds/webknossos/pull/6464)
 - Added workflow reporting and logging features for Voxelytics into webKnossos. If activated, the workflows can be accessed from the `Administration` > `Voxelytics` menu item. [#6416](https://github.com/scalableminds/webknossos/pull/6416) [#6460](https://github.com/scalableminds/webknossos/pull/6460)
 - Added possibility to read N5 datasets. [#6466](https://github.com/scalableminds/webknossos/pull/6466)
 - Added "shift + w" shortcut to cycle backwards through annotation tools. [#6493](https://github.com/scalableminds/webknossos/pull/6493)
@@ -553,7 +553,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Changed
 - Improved context menu for interactions with segmentation data that wasn't loaded completely, yet. [#5637](https://github.com/scalableminds/webknossos/pull/5637)
 - Any feature connected to computational jobs like precomputing a meshfile is now disabled for non local hosted datasets. [#5663](https://github.com/scalableminds/webknossos/pull/5663)
-- Clicking outside of the context menu closes it without performing any other action (e.g., previously, a node could be created when clicking outside of the context menu, when the skeleton tool was active). Also, a repeated rightclick doesn't open the context menu again. [#5658](https://github.com/scalableminds/webknossos/pull/5658)
+- Clicking outside of the context menu closes it without performing any other action (e.g., previously, a node could be created when clicking outside of the context menu, when the skeleton tool was active). Also, a repeated right-click doesn't open the context menu again. [#5658](https://github.com/scalableminds/webknossos/pull/5658)
 - When the option "Rendering missing data black" is turned of, the fallback data is now shown up to a zoom difference of 3. Previously it was 1. [#5674](https://github.com/scalableminds/webknossos/pull/5674)
 
 ### Fixed

diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -1,6 +1,6 @@
 # Changelog (Unreleased)
 
-All notable (yet unreleased) user-facing changes to webknossos are documented in this file.
+All notable (yet unreleased) user-facing changes to WEBKNOSSOS are documented in this file.
 See `CHANGELOG.released.md` for the changes which are part of official releases.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
@@ -18,6 +18,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Changed
 - Improved performance of opening a dataset or annotation. [#6711](https://github.com/scalableminds/webknossos/pull/6711)
 - Redesigned organization page to include more infos on organization users, storage, webKnossos plan and provided opportunities to upgrade. [#6602](https://github.com/scalableminds/webknossos/pull/6602)
+- Changed branding of WEBKNOSSOS including a new logo, new primary colors, and UPPERCASE name. [#6739](https://github.com/scalableminds/webknossos/pull/6739)
 
 ### Fixed
 - Fixed node selection and context menu for node ids greater than 130813. [#6724](https://github.com/scalableminds/webknossos/pull/6724) and [#6731](https://github.com/scalableminds/webknossos/pull/6731)

diff --git a/Contributing Guide.md b/Contributing Guide.md
@@ -1,12 +1,12 @@
 # Contributing Guide
 
-**Welcome to the webKnossos contributing guide :sparkles: **
+**Welcome to the WEBKNOSSOS contributing guide :sparkles: **
 
-Thank you for taking the time to contribute to this project! The following is a set of guidelines for contributing to webKnossos. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
+Thank you for taking the time to contribute to this project! The following is a set of guidelines for contributing to WEBKNOSSOS. These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
 
 ## Code of Conduct
 
-webKnossos and everyone contributing and collaborating on this project is expected to follow the [webKnossos Code of Conduct](CODE_OF_CONDUCT.md). Please report unacceptable behavior to [[email protected]](mailto:[email protected]).
+WEBKNOSSOS and everyone contributing and collaborating on this project is expected to follow the [WEBKNOSSOS Code of Conduct](CODE_OF_CONDUCT.md). Please report unacceptable behavior to [[email protected]](mailto:[email protected]).
 
 
 ## How can I help?
@@ -20,20 +20,20 @@ We welcome community feedback and contributions! We are happy to have
 
 ## Feedback, Observations and Questions
 
-We'd love to hear your feedback on the webKnossos!
+We'd love to hear your feedback on the WEBKNOSSOS!
 We're also interested in hearing if this tool don't work for your usecase,
 or if you have questions regarding its usage.
 
 Please leave a message on the [image.sc forum](https://forum.image.sc/tag/webknossos)
 using the `webknossos` tag to enable public communication on those topics.
-If you prefer to share information only with the webKnossos team, please write an email
+If you prefer to share information only with the WEBKNOSSOS team, please write an email
 to [[email protected]](mailto:[email protected]). For commercial support please
 reach out to [scalable minds](https://scalableminds.com).
 
 
 ## Issues: Feature Suggestions and Bug Reports
 
-We track feature requests and bug reports in the [webKnossos repository issues](https://github.com/scalableminds/webknossos/issues).
+We track feature requests and bug reports in the [WEBKNOSSOS repository issues](https://github.com/scalableminds/webknossos/issues).
 Before opening a new issue, please do a quick search of existing issues to make sure your suggestion hasn’t already been added.
 If your issue doesn’t already exist, and you’re ready to create a new one, make sure to state what you would like to implement, improve or bugfix.
 Please use one of the provided templates to make this process easier for you.
@@ -54,8 +54,8 @@ that you use the API as intended. If that's the case, please
 
 If you are missing a feature to support your use-case, please consider the following points:
 
-1. Please verify if this feature is directly related to webKnossos.
-   Does it belong into the webKnossos?
+1. Please verify if this feature is directly related to WEBKNOSSOS.
+   Does it belong into the WEBKNOSSOS?
 2. Double-check if an issue for this feature exists already. If there is one with a very similar scope,
    please considering commenting there.
 3. If possible, consider how the implementation might look like (e.g. how would the public API change),
@@ -88,7 +88,7 @@ Please include the following in your pull request:
 * Adapt or add the documentation.
 * Consider enhancing the examples.
 
-The specific coding styles, test frameworks and documentation setup of webKnossos are described
+The specific coding styles, test frameworks and documentation setup of WEBKNOSSOS are described
 in the following sections:
 
 
@@ -109,6 +109,6 @@ The [webknossos repository](https://github.com/scalableminds/webknossos) is stru
 
 ### Documentation
 
-We render a combined documentation for webKnossos itself and the webKnossos Python libraries from the webknossos-libs repository using [mkdocs](https://www.mkdocs.org/). Source-files for the documentation are stored in the `docs` directory.
+We render a combined documentation for WEBKNOSSOS itself and the WEBKNOSSOS Python libraries from the webknossos-libs repository using [mkdocs](https://www.mkdocs.org/). Source-files for the documentation are stored in the `docs` directory.
 
-The documentation is deploy automatically through GitHub actions from the [webKnossos Python libraries repository](https://github.com/scalableminds/webknossos-libs/actions).
+The documentation is deploy automatically through GitHub actions from the [WEBKNOSSOS Python libraries repository](https://github.com/scalableminds/webknossos-libs/actions).
diff --git a/DEV_INSTALL.md b/DEV_INSTALL.md
@@ -9,8 +9,8 @@ docker-compose pull webknossos
 ./start-docker.sh
 ```
 
-Open your local webKnossos instance on [localhost:9000](http://localhost:9000) and complete the onboarding steps in the browser.
-Now, you are ready to use your local webKnossos instance.
+Open your local WEBKNOSSOS instance on [localhost:9000](http://localhost:9000) and complete the onboarding steps in the browser.
+Now, you are ready to use your local WEBKNOSSOS instance.
 
 See the wiki for [instructions on updating](https://github.com/scalableminds/webknossos/wiki/Development-setup) this development setup.
 
@@ -29,7 +29,7 @@ For non-localhost deployments, check out the [installation guide in the document
 
 ### MacOS
 ```bash
-# webKnossos needs to be run from x86_64 environment (only applicable for arm64-based Macs)
+# WEBKNOSSOS needs to be run from x86_64 environment (only applicable for arm64-based Macs)
 arch -x86_64 /bin/zsh
 
 # Install Homebrew package manager
@@ -58,13 +58,13 @@ psql -c "CREATE USER postgres WITH ENCRYPTED PASSWORD 'postgres';"
 psql -c "ALTER USER postgres WITH SUPERUSER;"
 psql -c "GRANT ALL PRIVILEGES ON DATABASE webknossos TO postgres;"
 
-# Checkout the webKnossos git repository
+# Checkout the WEBKNOSSOS git repository
 git clone [email protected]:scalableminds/webknossos.git
 
 
 ```
 
-Note: On arm64-based Macs (e.g. M1), you need to run webKnossos in an x86_64 environment (Rosetta 2). In case you accidentally started webKnossos in an arm64 environment, it is advisable to delete several caches `~/.m2`, `~/ivy2`, `~/.sbt`, `~/.yarn-cache` and run `./clean`. Since Postgres and Redis are isolated processes, they can be run either from arm64 or x86_64 environments.
+Note: On arm64-based Macs (e.g. M1), you need to run WEBKNOSSOS in an x86_64 environment (Rosetta 2). In case you accidentally started WEBKNOSSOS in an arm64 environment, it is advisable to delete several caches `~/.m2`, `~/ivy2`, `~/.sbt`, `~/.yarn-cache` and run `./clean`. Since Postgres and Redis are isolated processes, they can be run either from arm64 or x86_64 environments.
 
 
 ### Ubuntu 20.04 LTS
@@ -121,9 +121,9 @@ First, install all frontend dependencies via
 ```bash
 yarn install
 ```
-Note: During this installation step, it might happen that the module `gl` cannot be installed correctly. As this module is only used for testing webKnossos, you can safely ignore this error.
+Note: During this installation step, it might happen that the module `gl` cannot be installed correctly. As this module is only used for testing WEBKNOSSOS, you can safely ignore this error.
 
-To start webKnossos, use
+To start WEBKNOSSOS, use
 ```bash
 yarn start
 ```

diff --git a/MIGRATIONS.released.md b/MIGRATIONS.released.md
@@ -1,5 +1,5 @@
 # Migration Guide (Released)
-All migrations of webKnossos are documented in this file.
+All migrations of WEBKNOSOSS are documented in this file.
 See `MIGRATIONS.unreleased.md` for the changes which are not yet part of an official release.
 
 This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.

diff --git a/MIGRATIONS.unreleased.md b/MIGRATIONS.unreleased.md
@@ -1,5 +1,5 @@
 # Migration Guide (Unreleased)
-All migrations (for unreleased versions) of webKnossos are documented in this file.
+All migrations (for unreleased versions) of WEBKNOSSOS are documented in this file.
 See `MIGRATIONS.released.md` for the migrations which are part of official releases.
 
 This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.

diff --git a/README.md b/README.md
@@ -1,13 +1,13 @@
-# [webKnossos](https://webknossos.org/)
-<img align="right" src="https://static.webknossos.org/images/oxalis.svg" alt="webKnossos Logo" />
-webKnossos is an open-source tool for annotating and exploring large 3D image datasets.
+# [WEBKNOSSOS](https://webknossos.org/)
+<img align="right" src="https://static.webknossos.org/images/icon-only.svg" alt="WEBKNOSSOS Logo" />
+WEBKNOSSOS is an open-source tool for annotating and exploring large 3D image datasets.
 
 * Fly through your data for fast skeletonization and proof-reading
 * Create 3D training data for automated segmentations efficiently
 * Scale data reconstruction projects with crowdsourcing workflows
 * Share datasets and annotations with collaborating scientists
 
-[Start using webKnossos](https://webknossos.org) - [On your own server](https://docs.webknossos.org/webknossos/installation.html) - [User Documentation](https://docs.webknossos.org) - [Contact us](mailto:[email protected])
+[Start using WEBKNOSSOS](https://webknossos.org) - [On your own server](https://docs.webknossos.org/webknossos/installation.html) - [User Documentation](https://docs.webknossos.org) - [Contact us](mailto:[email protected])
 
 [![](https://img.shields.io/circleci/project/github/scalableminds/webknossos/master.svg?logo=circleci)](https://circleci.com/gh/scalableminds/webknossos)
 [![](https://img.shields.io/github/release/scalableminds/webknossos.svg)](https://github.com/scalableminds/webknossos/releases/latest)
@@ -44,9 +44,9 @@ webKnossos is an open-source tool for annotating and exploring large 3D image da
 [Read more about the original publication.](https://publication.webknossos.org)
 
 ## Installation
-webKnossos is open-source, so you can install it on your own server.
+WEBKNOSSOS is open-source, so you can install it on your own server.
 
-[Check out the documentation](https://docs.webknossos.org/webknossos/installation.html) for a tutorial on how to install webKnossos on your own server.
+[Check out the documentation](https://docs.webknossos.org/webknossos/installation.html) for a tutorial on how to install WEBKNOSSOS on your own server.
 
 For development installations, please see `DEV_INSTALL.md` file.
 
@@ -61,17 +61,17 @@ For details on community contributions, please refer to our [Contributing guide]
 
 Contact us at [[email protected]](mailto:[email protected]).
 
-[scalable minds](https://scalableminds.com) offers commercial hosting, support and development services for webKnossos.
+[scalable minds](https://scalableminds.com) offers commercial hosting, support and development services for WEBKNOSSOS.
 
 
 ## Credits
 * scalable minds - https://scalableminds.com/
 * Max Planck Institute for Brain Research – https://brain.mpg.de/
 
-webKnossos was inspired by [KNOSSOS](https://knossos.app).
+WEBKNOSSOS was inspired by [KNOSSOS](https://knossos.app).
 
 ### Thanks
-* [Browser Stack](https://www.browserstack.com/) for letting us test webKnossos on a variety of different devices
+* [Browser Stack](https://www.browserstack.com/) for letting us test WEBKNOSSOS on a variety of different devices
   <a href="https://www.browserstack.com/"><img src="https://avatars.githubusercontent.com/u/1119453?s=200&v=4" width=100 alt="Browserstack Logo" align="right"></a>
 * [CircleCI](https://circleci.com/gh/scalableminds/webknossos) for letting us run builds and tests on their CI
 

diff --git a/app/controllers/Application.scala b/app/controllers/Application.scala
@@ -34,10 +34,10 @@ class Application @Inject()(multiUserDAO: MultiUserDAO,
   private lazy val Mailer =
     actorSystem.actorSelection("/user/mailActor")
 
-  @ApiOperation(value = "Information about the version of webKnossos")
+  @ApiOperation(value = "Information about the version of WEBKNOSSOS")
   @ApiResponses(
     Array(
-      new ApiResponse(code = 200, message = "JSON object containing information about the version of webKnossos"),
+      new ApiResponse(code = 200, message = "JSON object containing information about the version of WEBKNOSSOS"),
       new ApiResponse(code = 400, message = "Operation could not be performed. See JSON body for more information.")
     ))
   def buildInfo: Action[AnyContent] = sil.UserAwareAction.async {

diff --git a/app/controllers/InitialDataController.scala b/app/controllers/InitialDataController.scala
@@ -71,7 +71,7 @@ Samplecountry
       ObjectId.generate,
       "sample_organization",
       additionalInformation,
-      "/assets/images/oxalis.svg",
+      "/assets/images/icon-only.svg",
       "Sample Organization",
       PricingPlan.Custom,
       None,
@@ -132,7 +132,7 @@ Samplecountry
   private val defaultPublication = Publication(
     ObjectId("5c766bec6c01006c018c7459"),
     Some(Instant.now),
-    Some("https://static.webknossos.org/images/oxalis.svg"),
+    Some("https://static.webknossos.org/images/icon-only.svg"),
     Some("Dummy Title that is usually very long and contains highly scientific terms"),
     Some(
       "This is a wonderful dummy publication, it has authors, it has a link, it has a doi number, those could go here.\nLorem [ipsum](https://github.com/scalableminds/webknossos) dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua.")

diff --git a/app/controllers/OrganizationController.scala b/app/controllers/OrganizationController.scala
@@ -168,7 +168,7 @@ class OrganizationController @Inject()(organizationDAO: OrganizationDAO,
         defaultMails.upgradePricingPlanRequestMail(request.identity,
                                                    userEmail,
                                                    organization.displayName,
-                                                   "Extend webKnossos plan by a year"))
+                                                   "Extend WEBKNOSSOS plan by a year"))
     } yield Ok
   }
 
@@ -190,7 +190,7 @@ class OrganizationController @Inject()(organizationDAO: OrganizationDAO,
           defaultMails.upgradePricingPlanRequestMail(request.identity,
                                                      userEmail,
                                                      organization.displayName,
-                                                     s"Upgrade webKnossos Plan to $requestedPlan"))
+                                                     s"Upgrade WEBKNOSSOS Plan to $requestedPlan"))
       } yield Ok
   }