scalableminds / webknossos

Visualize, share and annotate your large 3D images online

WEBKNOSSOS

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 - On your own server - User Documentation - Contact us

Website and hosted version

https://webknossos.org

Features

• Exploration of large 3D image datasets
• Fully browser-based user experience with efficient data streaming
• Creation/editing of skeleton and volume annotations
• Innovative flight mode for fast skeleton annotation
• Optimized performance for large annotations
• User and task management for high-throughput crowdsourcing
• Sharing and collaboration features
• Proof-Reading tools for working with large (over)-segmentations
• Standalone datastore component for flexible deployments
• Supported dataset formats: WKW, Neuroglancer Precomputed, Zarr, N5
• Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel
• Support for 3D mesh rendering and ad-hoc mesh generation
• Export and streaming of any dataset and annotation as Zarr to third-party tools
• Documented frontend API for user scripts, REST API for backend access
• Open-source development with automated test suite
• Docker-based deployment for production and development
• Detailed Documentation

Publication

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.

Read more about the original publication.

Installation

WEBKNOSSOS is open-source, so you can install it on your own server.

Check out the documentation for a tutorial on how to install WEBKNOSSOS on your own server.

For development installations, please see DEV_INSTALL.md file.

Contributions, Contact and Support

We welcome community feedback and contributions! We are happy to have

• general feedback, observations and questions on the image.sc forum,
• feature suggestions and bug reports as issues on GitHub,
• documentation, examples and code contributions as pull requests on GitHub.

For details on community contributions, please refer to our Contributing guide.

Contact us at [email protected].

scalable minds 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.

Thanks

• Browser Stack for letting us test WEBKNOSSOS on a variety of different devices
• CircleCI for letting us run builds and tests on their CI

License

AGPLv3

webknossos's Issues

[OX-679] Show warning if nml scale differs from dataSet scale

[reporter="tmbo", created="Mon, 10 Jun 2013 12:10:37 +0200"]

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[OX-677] Load hidden dashboard information on demand via ajax

[reporter="tmbo", created="Mon, 10 Jun 2013 00:16:05 +0200"]

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[OX-591] task list loading speed suggestion

[reporter="autoreporter", created="Thu, 11 Apr 2013 19:08:49 +0200"]

Hi,
wenn ich die Task Liste in Oxalis öffnen möchte lädt das immer eine ganze Weile. Je mehr Aufgaben in Zukunft dazu kommen, desto umständlicher wird das. Ich würde daher vorschlagen, dass die Inhalte der ganzen Reiter (also die einzelnen Tracings der Nutzer zu jedem Task) nicht immer alle geladen werden, sondern nur auf Anfrage wenn der entsprechende Reiter geöffnet wird.
Grüße
Fabian

Reported by: Fabian Isensee ([email protected])

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[OX-290] Show all users logged times on a view

[reporter="tmbo", created="Sun, 6 Jan 2013 00:52:41 +0100"]

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[OX-548] Hack edge thickness in Windows

[reporter="autoreporter", created="Thu, 28 Mar 2013 14:43:03 +0100"]

So as Daniel told me, setting the edge thickness of a particle Windows is not possible.
From time to time, I really need thicker edges though.
Here is what I would like to use instead:
Pressing "0" would increases the browser zoom level to 500%.
All controls would have to be scaled accordingly, or if that's not easily possible, not showed at all.
The viewport size would be set to 20%

Pressing "0" again would reset everything to where it was before. (Zoom 100%, Viewport size 100%)

Reported by: Kevin Boergens ([email protected])

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[OX-676] Improve page load performance

[reporter="tmbo", created="Mon, 10 Jun 2013 00:12:43 +0200"]

To increase the page loading speed some improvements need to be made:

• minify & optimize js
• lazy load information which is not displayed initially on page load

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[OX-761] Time-Tracker

[reporter="philipp.otto", created="Tue, 20 Aug 2013 01:59:44 +0200"]

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[OX-320] Volume Tracing

[reporter="georg", created="Fri, 11 Jan 2013 18:00:03 +0100"]

Main Issue to collect volume tracing sub tasks

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[OX-542] Chat

[reporter="autoreporter", created="Sat, 23 Mar 2013 13:27:27 +0100"]

We want to get a feel for what can be done with a chat and Oxalis is a good test environment for that.
Everybody logged in should be a member of the chat. But it should be possible to opt out if one needs to work in a concentrated fashion.
All chat should be logged and accessible to the admins.
Are there chat components ready you could include into Oxalis without having to do all of it yourself?

Reported by: Kevin Boergens ([email protected])

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[OX-755] oxalis db coexistence with levelcreators replicated database

[reporter="tewe", created="Fri, 16 Aug 2013 21:23:04 +0200"]

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[OX-659] Save Bounding Box with task

[reporter="georg", created="Fri, 31 May 2013 11:11:20 +0200"]

Admins should be able to optionally set a bounding box when creating a task. Also, this can be edited by the user (as in OX-553.oxalis.at, View->bounding Box). The input format used in Klee is "x, x, y, y, z, z", I think it could just be passed as a string, since I need to parse it anyway.

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[OX-732] Zooming in and out repeatedly lets oxalis crash

[reporter="tmbo", created="Mon, 5 Aug 2013 15:48:58 +0200"]

1. Go in the tracing view
2. Zoom in and out repeatedly using ALT+Trackpad
3. Chromes "Oh nein!" gets shown

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[OX-604] Repair Firefox-Support

[reporter="johannes", created="Tue, 16 Apr 2013 21:03:50 +0200"]

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[OX-766] Merge several branches into dev, test

[reporter="georg", created="Wed, 21 Aug 2013 21:26:16 +0200"]

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[OX-637] Bulk list of admin interactions

[reporter="autoreporter", created="Tue, 7 May 2013 16:55:24 +0200"]

Today, we needed to find out who created a specific task.
Is it possible to access a log of all admin interactions?
Like:
2013-05-07 16:43: [email protected] task 054e3a changed instances to 3
That would be good

Reported by: Kevin Boergens ([email protected])

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[OX-366] [Volume Tracing] Server-Client communication

[reporter="georg", created="Sat, 26 Jan 2013 13:11:03 +0100"]

We need to define what information is transmitted in what format and implement the communication.

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[OX-454] mongodb - auth

[reporter="tewe", created="Sat, 23 Feb 2013 00:51:29 +0100"]

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[OX-763] Introduce to Binary part of oxalis

[reporter="georg", created="Tue, 20 Aug 2013 21:21:49 +0200"]

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[OX-673] nml download in read only mode doesn't work

[reporter="autoreporter", created="Sun, 9 Jun 2013 00:50:18 +0200"]

which killed 30 minutes of my studious tracings..........

Reported by: Moritz Helmstädter ([email protected])

Way to solve this:
when editing read only annotations a click on NML download should result in the client pushing all trees + nodes + edges to the server which creates a NML file for the client to download (without storing the trees)

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[OX-275] Mouse wheel navigation

[reporter="autoreporter", created="Tue, 18 Dec 2012 19:51:06 +0100"]

When using mouse wheel for dataset navigation, an impulse from the mouse wheel should always be translated in a 1 voxel movement (like a single d or f press)

Reported by: Kevin Boergens ([email protected])

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[OX-224] Display active Node ID

[reporter="autoreporter", created="Mon, 3 Dec 2012 22:29:03 +0100"]

It would be nice to have a feature where you can activate all node IDs to be shown like in Knossos.

Reported by: Tobias Ruff ([email protected])

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[OX-683] Switch between active nodes

[reporter="autoreporter", created="Tue, 18 Jun 2013 12:00:55 +0200"]

Hi,

I was just wondering, would it be possible ( or does it already exist) to have some sort of keyboard shortcut to move between active nodes? Like shift+left or right arrow, or something to that effect? Would make commenting a lot easier too.

best,
Iris

Reported by: Iris Yu ([email protected])

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[OX-743] Include Breeze

[reporter="tewe", created="Mon, 12 Aug 2013 15:32:45 +0200"]

replace linear algebra stuff

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[OX-279] Refactor actor creation and reference handling

[reporter="tmbo", created="Wed, 2 Jan 2013 10:32:38 +0100"]

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[OX-668] Automatische Email an Adminteam wenn eine Trainingszelle als Finish markiert wurde

[reporter="autoreporter", created="Wed, 5 Jun 2013 14:28:40 +0200"]

Hey,

Wir haben jetzt seit ein paar Wochen Trainingszellen auf Oxalis gestellt (Project: Oxalis Training, Admin Annette Gäbelein). Jetzt haben wir das Problem, dass wir nicht mehr Benachrichtigt werden wenn ein Hiwi seine Trainingszelle als Finish markiert. Wir haben den Hiwis mitgeteilt, dass sie uns eine Mail schicken sollen wenn sie dies getan haben. Ich finde diesen Weg sehr umständlich. Außerdem wird so die eine oder andere Trainingszelle leicht übersehen. Ist es möglich eine automatische Mail an uns ([email protected]) zu senden, wenn ein Hiwi seine Trainingszelle als Finish markiert hat? Dadurch würde bei uns im Issuetracker ein neuer Issue entstehen. So könnten wir den Weg von abgegebener und verbesserter Trainingszelle verkürzen/optimieren.

Vielen Dank für eure Hilfe!

Best,
Alex

Reported by: Alexander Häusl ([email protected])

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[OX-660] Huge number of data requests when not moving

[reporter="tmbo", created="Fri, 31 May 2013 17:18:21 +0200"]

Steps to reproduce:

• trace a little around
• stop tracing and watch the network tab
• for example: I traced 5 min and after I stopped another 3317 Requests got send downloading 133MB

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[OX-747] Can't delete project

[reporter="autoreporter", created="Tue, 13 Aug 2013 14:41:46 +0200"]

I tried to delete the project 1 active but that's not possible

Reported by: Kevin Boergens ([email protected])

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[OX-20] ping strategies

[reporter="johannes", created="Wed, 8 Aug 2012 19:57:08 +0200"]

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[OX-663] Implement RGB-support

[reporter="johannes", created="Sat, 1 Jun 2013 14:55:07 +0200"]

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[OX-661] Measure buckets / kb loaded and report to server

[reporter="johannes", created="Sat, 1 Jun 2013 14:53:26 +0200"]

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[OX-730] Create MongoDB Evolution Plugin

[reporter="tmbo", created="Sun, 28 Jul 2013 14:53:07 +0200"]

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[OX-656] Passwortänderung

[reporter="autoreporter", created="Mon, 27 May 2013 15:50:03 +0200"]

Es kamen ein paar Mal Anfragen ob es möglich wäre das Passwort im Nachhinein nochmals zu ändern, ließe sich eine entsprechende Funktion einbauen?

Viele Grüße, Annette

Reported by: Annette Gäbelein ([email protected])

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[OX-770] Create Bulk action for team administration in the user table

[reporter="tmbo", created="Mon, 26 Aug 2013 13:31:49 +0200"]

Should behave pretty similar to the roles assignment. After clicking on the action in the bulk menu the overlay should poput and let one define all the groups the selected useres should be part of. The multiselect menu can be copied from the verification form.

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[OX-633] Switch to reactive mongo as DB driver

[reporter="tmbo", created="Sat, 4 May 2013 15:47:05 +0200"]

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[OX-693] Finish for finished tasks

[reporter="autoreporter", created="Tue, 25 Jun 2013 00:44:45 +0200"]

When opening a finished tracing (eg 1c55c5 (tracing by Marco Reiner)), it is possible to click finish, which doesn't make exactly sense

Best,
Kevin

Reported by: MHLab Iris Natalia Kevin shared ([email protected])

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[OX-754] binarydata upload via sftp and password for mhlab

[reporter="tewe", created="Fri, 16 Aug 2013 21:21:50 +0200"]

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[OX-664] Restructure and extend model for volume tracing

[reporter="johannes", created="Sat, 1 Jun 2013 14:55:49 +0200"]

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[OX-742] Oxalis dataset watcher crashes upon faulty json

[reporter="tewe", created="Mon, 12 Aug 2013 14:28:11 +0200"]

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[OX-750] Provide correct dataset descriptions

[reporter="daniel", created="Wed, 14 Aug 2013 20:19:36 +0200"]

Provide correct dataset descriptions on oxalis.at/datasets.

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[OX-678] Optimize code to work properly with require JS optimization

[reporter="tmbo", created="Mon, 10 Jun 2013 00:17:25 +0200"]

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[OX-636] Mail notification on double request

[reporter="autoreporter", created="Mon, 6 May 2013 09:36:16 +0200"]

Please send out a mail to [email protected] if someone requests a task although they still have one.

Reported by: Kevin Boergens ([email protected])

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[OX-728] Overview is broken

[reporter="tmbo", created="Sun, 28 Jul 2013 13:36:31 +0200"]

Admin->Tasks->Overview is broken again (master). Please also include the proper panning / zooming from project-zoom.

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[OX-647] Nodes not Visible anymore in classical mode on top Screens

[reporter="autoreporter", created="Sun, 19 May 2013 20:34:32 +0200"]

I have a bug which only appears on my laptop. The nodes on the two top screens (XY, YZ) of the classical mode are not displayed anymore. I can still see the rig-sceleton, which connects the nodes, but not the nodes themselves. The bottow window (XZ) shows the nodes as usually, and I can change their size with shift + mousewheel / in the options menu. Since I was not sure on which basis Oxalis is running, I reinstalled Java, Flash and Google Chrome. Anyway nothing changed, and this only appears when using my laptop.

Reported by: Helge Feddersen ([email protected])

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[OX-658] working hour count

[reporter="autoreporter", created="Wed, 29 May 2013 13:06:40 +0200"]

The working hours are not counted if you just move along the trees searching for e.g. synapses.

Reported by: Initial Segment Overview ([email protected])

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[OX-564] Projects don't recognize owners

[reporter="autoreporter", created="Thu, 4 Apr 2013 00:18:10 +0200"]

I tried changing a task that was of a project I'm not the owner of. This should have a warning message that I'm changing stuff that might be none of my business

Reported by: Kevin Boergens ([email protected])

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[OX-771] Try out hip-chat jquery plugin on oxalis

[reporter="tmbo", created="Mon, 26 Aug 2013 23:21:39 +0200"]

Please have a look if we can use this plugin as an oxalis chat.

http://blog.hipchat.com/2013/08/20/embedding-hipchat/

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[OX-753] Show warn message on admin->datasets if the dataset has no settings / layer.json

[reporter="tmbo", created="Fri, 16 Aug 2013 18:39:18 +0200"]

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[OX-357] Miscellaneous works

[reporter="daniel", created="Thu, 24 Jan 2013 03:40:31 +0100"]

This issue should be used to log time for miscellaneous oxalis related tasks, as setting up and maintaining the development environment, update procedures (play etc.), e-mail conversations and so on, which are issue-independent, but still take their time.

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[OX-724] Move brightness/contrast to shader

[reporter="johannes", created="Thu, 25 Jul 2013 17:16:18 +0200"]

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[OX-11] new realoading

[reporter="johannes", created="Wed, 8 Aug 2012 19:56:01 +0200"]

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