Updates to wK Docs #5995

hotzenklotz · 2022-01-27T16:09:47Z

I updated the wK Docs to include new features, refine texts, remove outdated information, and reorganize stuff to match the current state of webKnossos. I ran grammarly on these changes to catch as many typos and mistakes as possible, but there might be some remaining.

New pages:

Automated Analysis
Processing Jobs
FAQ

Images/Screenshots will also be updated by @lilliber in separate PRs. That should not block us from releasing this PR though.

While I tried to write all the new changes as consistently as possible, I am aware that we go back between active and passive voice quite often. Since I did not want to re-write the whole docs and turn the PR into a novel I suggest to YOLO.
I also put more focus on documenting wk.org features as it is the best wK user experience.

Steps to test:

RTFM

Issues:

none
see also wk-libs PR to update docs navigation bar to include the new page: Add more pages to navigation for webKnossos docs webknossos-libs#609

(Please delete unneeded items, merge only when none are left open)

Updated (unreleased) changelog
Updated (unreleased) migration guide if applicable
Updated documentation if applicable
Adapted wk-connect if datastore API changes
Adapted wk-libs python client if relevant API parts change
Needs datastore update after deployment
Ready for review

* 'master' of github.com:scalableminds/webknossos: fix positioning of clip button (#5992) Honor mappingStatus when requesting to compute meshes ad-hoc (#5982) Add UI to globalize incomplete floodfill(s) (#5905) Add auto scaling for color layer (#5961) Fix placeholder resolutions for anisotropic layers with missing base resolutions (#5983) Fix dashboard refresh button behaviour (#5971) Update nanoid, trim-off-newlines and node-fetch (#5979) Add Arthur’s Alias in Build Notification Script (#5943) fix nml upload by providing process browser shim (#5987)

* 'master' of github.com:scalableminds/webknossos: Add option to change active segement (#6006) ship expanded testdata (#6004) Allow Download of Public Annotations While Logged Out (#6001) Increase maximum bucket count limit for segmentation layers (#6000) Allow cancelling uploads (#5958) Store layer visibility with annotation (#5967) Fix async volume bugs (#5955)

* 'master' of github.com:scalableminds/webknossos: Log legacy route usages (#6024) Change GET routes with side effects to POST (#6023) More api swagger annotations (#5989) add shorthand for deleting trees (#6013) Added shorthand to mark branch points from context menu (#6012) Map node group context menu to right-click (#6021) For empty volume tracings, serve header-only zip (#6022) use allDataBlocking and temporary files for explorative download (#6009)

…ssos into docs * 'docs' of github.com:scalableminds/webknossos: * 'master' of github.com:scalableminds/webknossos: Split cells via Min Cut (#5885) Clean up backend util package (#6048) Guard against empty saves (#6052) Time tracking: Do not fail on empty timespans list (#6051) Fix clip button changing position (#6050) Include ParamFailure values in error chains (#6045) Fix non-32-aligned bucket requests (#6047) Don't enforce save state when saving is triggered by a timeout and reduce tracing layout analytics event count (#5999) Bump cached-path-relative from 1.0.2 to 1.1.0 (#5994) Volume annotation download: zip with BEST_SPEED (#6036) Sensible scalebar values (#6034) Faster CircleCI builds (#6040) move to Google Analytics 4 (#6031) Fix nightly (fix tokens, upgrade puppeteer) (#6032) Add neuron reconstruction job backend and frontend part (#5922) Allow uploading multi-layer volume annotations (#6028)

* 'master' of github.com:scalableminds/webknossos: Release 22.03 (#6069) Skip deactivated users in dataset access list (#6070) Compile tests to different dir to avoid unnecessary recompilations (#6065) Add loaded meshes to sharing link (#5993)

hotzenklotz · 2022-02-22T15:59:11Z

docs/sharing.md


-webKnossos shares datasets publicly (everyone can view them without any login) or privately (a login or special URLs are required to view the link).
+## Sharing 
+As mentioned earlier, any webKnossos resource can be shared as a normal web URL. The easiest way to obtain this sharing link is by clicking the `Share` button in the toolbar at the top of the screen next to the position/coordinate section (*Share icon*). 


I started with this section thinking dataset and annotation sharing work the same way... Then I gave up... might want to remove this section of merge it with other stuff.

Yep, this seems redundant. Maybe call the section "Dataset sharing"?

This section does not describe dataset sharing. These options are not available for datasets. only for annotations. its confusing.

But what is this section for? There is another "Annotation sharing" section

hotzenklotz · 2022-02-22T16:03:49Z

@normanrz @philippotto I think I am done writing for now. 🤯Feel free to review. Perhaps, split the reading parts or invite more people to read if you like.

I am sure there is more stuff that is still missing or lacking. Also the writing style of the docs are all over the place... but you can have it all :-P
There are some TODO comments for more image, but those will be added by @lilliber in due time.

I am also not happy with the page on Sharing. This requires some big brain moments. Perhaps someone wants to refine that some more.

@normanrz Please double-check and expand the index page as that is the default landing page for the docs.

philippotto · 2022-02-23T14:50:48Z

philippotto

Great stuff 👍 I'm through with "my part" of the review and left a couple of suggestions.

docs/automated_analysis.md

docs/dashboard.md

docs/datasets.md

docs/mesh_visualization.md

docs/sharing.md

docs/tracing_ui.md

docs/users.md

docs/volume_annotation.md

Co-authored-by: Norman Rzepka <[email protected]>

* 'docs' of github.com:scalableminds/webknossos: Update docs/tooling.md Update docs/tasks.md

Co-authored-by: Norman Rzepka <[email protected]>

* 'docs' of github.com:scalableminds/webknossos: Update docs/tracing_ui.md

* 'docs' of github.com:scalableminds/webknossos: Connectome Tab (#5894) Fix duplicating annotations via toggling show archived annotations button and fix downsample modal rendering errors (#6058)

philippotto

Excellent! Only see my last few suggestions before merging.

philippotto · 2022-03-04T09:14:48Z

docs/users.md

@@ -82,6 +82,13 @@ On webKnossos.org, users can either sign up for a webKnossos account by themselv

    ![Send an invite link to new users](./images/users_invite.png)

+## Switching Organizations
+A webKnossos user account can be part of more than one organization, .e.g., when your are invtited to collaborate on projects of another institute, working as a different webKnossos organization.


Suggested change

A webKnossos user account can be part of more than one organization, .e.g., when your are invtited to collaborate on projects of another institute, working as a different webKnossos organization.

A webKnossos user account can be part of more than one organization, e.g., when your are invited to collaborate on projects of another institute, working as a different webKnossos organization.

philippotto · 2022-03-04T09:15:10Z

docs/users.md

+A webKnossos user account can be part of more than one organization, .e.g., when your are invtited to collaborate on projects of another institute, working as a different webKnossos organization.
+
+If you are part of multiple organizations, you can switch between them from the "User avatar" menu. 
+Click, on your user avatar in the top-right corner of the screen and select an entry from the "Switch Organization" menu.


Suggested change

Click, on your user avatar in the top-right corner of the screen and select an entry from the "Switch Organization" menu.

Click on your user avatar in the top-right corner of the screen and select an entry from the "Switch Organization" menu.

philippotto · 2022-03-04T09:17:29Z

docs/skeleton_annotation.md

@@ -136,7 +136,8 @@ Common tree operations include splitting and merging trees.
 #### Tree Colors
 A random color is assigned to each tree upon creation.
 Colors can be shuffled for a single tree or for all trees in a skeleton.
-Use the overflow menu under `More` in the `Skeleton` tab and select `Change Color` or `Shuffle All Colors` to assign new randomly chosen colors.
+Right-click on a tree to bring up several actions, .e.g `Shuffle Color`. 


Suggested change

Right-click on a tree to bring up several actions, .e.g `Shuffle Color`.

Right-click on a tree to bring up several actions, e.g. `Shuffle Color`.

philippotto · 2022-03-04T09:21:15Z

docs/sharing.md

-3. `Public`: Everybody, regardless their login status, can access this annotation.
-4. (`Team Sharing`: Share this annotation with other organization members on the dashboard in the `Shared Annotations` tab)
+ The easiest way to obtain this sharing link is by clicking the `Share` button in the toolbar at the top of the screen next to the position/coordinate section (*Share icon*). 
+ In any case, the sharing link also encodes additional information, such as your current camera position/rotation, zoom level, any layers that are turned on/off, the selected node, etc ([Details below](#sharing_link_format). In other words, a sharing link typically captures your current webKnossos state so that any recipient can take off from the same situation.


Suggested change

In any case, the sharing link also encodes additional information, such as your current camera position/rotation, zoom level, any layers that are turned on/off, the selected node, etc ([Details below](#sharing_link_format). In other words, a sharing link typically captures your current webKnossos state so that any recipient can take off from the same situation.

The sharing link also encodes additional information, such as your current camera position/rotation, zoom level, any layers that are turned on/off, the selected node, etc ([Details below](#sharing_link_format). In other words, a sharing link typically captures your current webKnossos state so that any recipient can take off from the same situation.

philippotto · 2022-03-04T09:21:57Z

docs/sharing.md


-In any case, the sharing link also encodes additional information, such as your current camera position/rotation, zoom level, any layers that are turned on/off, the selected node, etc ([Details below](#sharing_link_format). In other words, a sharing link typically captures your current webKnossos state so that any recipient can take off from the same situation.
+ Sharing a dataset is useful for multiple scenarios: 
+ - You recorded a novel microscopy dataset and want to include links to it in your paper or for reviewers. Use wklink.org to shorten these URLs, e.g. https://wklink.org/5386 ([contact us](mailto:[email protected])).


Suggested change

- You recorded a novel microscopy dataset and want to include links to it in your paper or for reviewers. Use wklink.org to shorten these URLs, e.g. https://wklink.org/5386 ([contact us](mailto:[email protected])).

- You recorded a novel microscopy dataset and want to include links to it in your paper or for reviewers. Use wklink.org to shorten these URLs, e.g. https://wklink.org/5386 ([contact us](mailto:[email protected]) to create these shortlinks).

philippotto · 2022-03-04T09:25:48Z

philippotto · 2022-03-04T09:26:02Z

Sorry, didn't see the automerge when I accepted.

* 'master' of github.com:scalableminds/webknossos: Updates to wK Docs (#5995)

* docs: mpre pr feedback Updates to wK Docs (#5995) restored some sections in sharing docs added context-menu hint to shortcuts more pr feedback Connectome Tab (#5894) Fix duplicating annotations via toggling show archived annotations button and fix downsample modal rendering errors (#6058)

* master: fix docs formatting Remove experimental auto brush feature (#6107) Fix markdown issues in docs (#6105) Unify long-running RPC timeouts (#6103) Disallow deactivating users with active tasks (#6099) Add remote origin headers also in error case (#6098) Linking layers during upload no longer restricted to public datasets (#6097) Fix layer headers layout (#6087) Fix more docs links (#6095) Update datasets.md (#6094) More PR feedback for Docs (#6091) Updates to wK Docs (#5995) Connectome Tab (#5894) Fix duplicating annotations via toggling show archived annotations button and fix downsample modal rendering errors (#6058)

hotzenklotz added 5 commits January 25, 2022 16:47

updates to the docs

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more documentation updates

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updates to docs

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more updates to docs

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hotzenklotz self-assigned this Jan 27, 2022

hotzenklotz added the documentation label Jan 27, 2022

hotzenklotz added 7 commits January 28, 2022 14:11

more docs

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more docs

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more docs

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WIP sharing

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hotzenklotz mentioned this pull request Feb 22, 2022

Add more pages to navigation for webKnossos docs scalableminds/webknossos-libs#609

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hotzenklotz added 8 commits February 22, 2022 16:41

updated datasets

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updated datasets docs

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applied many suggestions from grammarly

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add docs for jobs

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more docs

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restored typechange for changelog

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docs/CHANGELOG.released.md

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hotzenklotz commented Feb 22, 2022

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hotzenklotz marked this pull request as ready for review February 22, 2022 16:03

hotzenklotz requested review from normanrz and philippotto February 22, 2022 16:04

philippotto reviewed Feb 25, 2022

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normanrz reviewed Mar 1, 2022

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hotzenklotz and others added 17 commits March 2, 2022 10:11

Update docs/mesh_visualization.md

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Co-authored-by: Norman Rzepka <[email protected]>

Update docs/mesh_visualization.md

1de695c

Co-authored-by: Norman Rzepka <[email protected]>

Update docs/sharing.md

864aadf

Co-authored-by: Norman Rzepka <[email protected]>

Update docs/tracing_ui.md

b30dc20

Co-authored-by: Norman Rzepka <[email protected]>

Update docs/volume_annotation.md

d417e59

Co-authored-by: Norman Rzepka <[email protected]>

Update docs/volume_annotation.md

d447960

Co-authored-by: Norman Rzepka <[email protected]>

Update docs/tasks.md

c356061

Co-authored-by: Norman Rzepka <[email protected]>

Update docs/tooling.md

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Co-authored-by: Norman Rzepka <[email protected]>

more pr feedback

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Merge branch 'docs' of github.com:scalableminds/webknossos into docs

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* 'docs' of github.com:scalableminds/webknossos: Update docs/tooling.md Update docs/tasks.md

Update docs/tracing_ui.md

e7e0983

Co-authored-by: Norman Rzepka <[email protected]>

more pr feedback

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Merge branch 'docs' of github.com:scalableminds/webknossos into docs

b6dc872

* 'docs' of github.com:scalableminds/webknossos: Update docs/tracing_ui.md

Merge branch 'master' into docs

6e90644

added context-menu hint to shortcuts

160a16c

restored some sections in sharing docs

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hotzenklotz enabled auto-merge (squash) March 3, 2022 13:44

hotzenklotz requested review from normanrz and philippotto March 3, 2022 14:15

philippotto approved these changes Mar 4, 2022

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hotzenklotz merged commit 082e4c3 into master Mar 4, 2022

hotzenklotz deleted the docs branch March 4, 2022 09:24

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Merge branch 'master' of github.com:scalableminds/webknossos into docs

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* 'master' of github.com:scalableminds/webknossos: Updates to wK Docs (#5995)

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philippotto commented Mar 4, 2022

	A webKnossos user account can be part of more than one organization, .e.g., when your are invtited to collaborate on projects of another institute, working as a different webKnossos organization.
	A webKnossos user account can be part of more than one organization, e.g., when your are invited to collaborate on projects of another institute, working as a different webKnossos organization.

	Click, on your user avatar in the top-right corner of the screen and select an entry from the "Switch Organization" menu.
	Click on your user avatar in the top-right corner of the screen and select an entry from the "Switch Organization" menu.

	Right-click on a tree to bring up several actions, .e.g `Shuffle Color`.
	Right-click on a tree to bring up several actions, e.g. `Shuffle Color`.

	In any case, the sharing link also encodes additional information, such as your current camera position/rotation, zoom level, any layers that are turned on/off, the selected node, etc ([Details below](#sharing_link_format). In other words, a sharing link typically captures your current webKnossos state so that any recipient can take off from the same situation.
	The sharing link also encodes additional information, such as your current camera position/rotation, zoom level, any layers that are turned on/off, the selected node, etc ([Details below](#sharing_link_format). In other words, a sharing link typically captures your current webKnossos state so that any recipient can take off from the same situation.

	- You recorded a novel microscopy dataset and want to include links to it in your paper or for reviewers. Use wklink.org to shorten these URLs, e.g. https://wklink.org/5386 ([contact us](mailto:[email protected])).
	- You recorded a novel microscopy dataset and want to include links to it in your paper or for reviewers. Use wklink.org to shorten these URLs, e.g. https://wklink.org/5386 ([contact us](mailto:[email protected]) to create these shortlinks).

Updates to wK Docs #5995

Updates to wK Docs #5995

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hotzenklotz commented Jan 27, 2022 • edited Loading

Steps to test:

Issues:

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philippotto commented Mar 4, 2022

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