Updated documentation #7439

hotzenklotz · 2023-11-14T15:15:40Z

PR updates the WK docs:

new page for pen tablets / wacom / iPad
new page for creating animations
content for segment stats
re-structuring of the various data source into individual pages
several suggestions from gpt4 to various pages. mostly switching sentences from a passive to an active voice
small fixes here and there

URL of deployed dev instance (used for testing):

https://___.webknossos.xyz

Steps to test:

RTFM

DO NOT MERGE WITHOUT WK_LIBS PR

WIP Update Documentation webknossos-libs#965

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

Updated changelog
Updated migration guide if applicable
Updated documentation if applicable
Adapted wk-libs python client if relevant API parts change
Removed dev-only changes like prints and application.conf edits
Considered common edge cases
Needs datastore update after deployment

hotzenklotz · 2023-11-17T10:10:03Z

docs/animations.md

+
+A picture is worth a thousand words. In this spirit, you can use WEBKNOSSOS to create eye-catching animation of your datasets as a video clip. You can use these short movies as part of a presentation, website, for social media or to promote a publication.
+
+// animation video


hotzenklotz · 2023-11-17T10:11:09Z

docs/tooling.md

Most of these libs are deprecated. Probably not worht having a whole page and take up space in the navbar

normanrz · 2023-11-17T14:06:06Z

docs/animations.md

@@ -0,0 +1,19 @@
+# Animations
+
+A picture is worth a thousand words. In this spirit, you can use WEBKNOSSOS to create eye-catching animation of your datasets as a video clip. You can use these short movies as part of a presentation, website, for social media or to promote a publication.


Suggested change

A picture is worth a thousand words. In this spirit, you can use WEBKNOSSOS to create eye-catching animation of your datasets as a video clip. You can use these short movies as part of a presentation, website, for social media or to promote a publication.

A picture is worth more than a thousand words. In this spirit, you can use WEBKNOSSOS to create an eye-catching animation of your datasets as a video clip. You can use these short movies as part of a presentation, website, for social media or to promote a publication.

"more than" is Genglish: https://en.wikipedia.org/wiki/A_picture_is_worth_a_thousand_words

docs/animations.md

docs/dashboard.md

docs/datasets.md

docs/zarr.md

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

hotzenklotz · 2023-11-20T13:53:55Z

docs/n5.md

+WEBKNOSSOS expects the following file structure for N5 datasets:
+
+```
+my_dataset.n5             # One root folder per dataset


@fm3 @frcroth Is this structure for N5 correct?

Kinda. Webknossos can explore links to N5 datasets with an attributes.json that contains "multiscales" metadata, which points to the different actual arrays. This corresponds to our "mag" concept.

It can also explore N5 links to individual arrays (like, just one mag)

What you describe here looks more like our "layer" concept, but has nothing with "mags"/"multiscales". Instead, when the user has multiple n5 arrays (that are not just different multiscales/mags), they will have to input their URIs individually in webknossos.

hotzenklotz · 2023-11-20T13:54:09Z

docs/neuroglancer_precomputed.md

+WEBKNOSSOS expects the following file structure for Neuroglancer Precomputed datasets:
+
+```
+my_dataset.precomputed             # One root folder per dataset


@fm3 @frcroth Is this structure for Precomputed correct?

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

…s_update

hotzenklotz · 2023-11-22T12:46:20Z

@normanrz I added the feedback. PR still needs approval

normanrz

Looks good. Would be good to clarify the N5 questions, tho.

fm3

Sorry, looks like I never hit “submit” on these comments 🙈

fm3 · 2023-11-21T10:30:34Z

docs/n5.md

+
+WEBKNOSSOS can read [N5 datasets](https://github.com/saalfeldlab/n5).
+
+!!!info


I think only with full datasource-properties.json and everything

fm3 · 2023-11-21T10:37:04Z

docs/n5.md

+WEBKNOSSOS expects the following file structure for N5 datasets:
+
+```
+my_dataset.n5             # One root folder per dataset


Kinda. Webknossos can explore links to N5 datasets with an attributes.json that contains "multiscales" metadata, which points to the different actual arrays. This corresponds to our "mag" concept.

It can also explore N5 links to individual arrays (like, just one mag)

What you describe here looks more like our "layer" concept, but has nothing with "mags"/"multiscales". Instead, when the user has multiple n5 arrays (that are not just different multiscales/mags), they will have to input their URIs individually in webknossos.

updated docs

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hotzenklotz self-assigned this Nov 14, 2023

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hotzenklotz added 2 commits November 15, 2023 10:51

docs update #2

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applied some gpt4 feedback

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WIP Update Documentation scalableminds/webknossos-libs#965

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moar docs

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hotzenklotz commented Nov 17, 2023

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hotzenklotz changed the title ~~WIP: Updated documentation~~ Updated documentation Nov 20, 2023

hotzenklotz and others added 8 commits November 20, 2023 10:27

Update docs/dashboard.md

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

Update docs/datasets.md

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Update docs/datasets.md

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Update docs/datasets.md

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Update docs/zarr.md

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Update docs/zarr.md

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Update docs/zarr.md

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Update docs/zarr.md

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hotzenklotz added 2 commits November 20, 2023 14:57

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

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…s_update

added PR feedback

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hotzenklotz marked this pull request as ready for review November 20, 2023 14:23

hotzenklotz added 2 commits November 22, 2023 13:40

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

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…s_update

added example video for animations

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Updated documentation #7439

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fm3 Nov 21, 2023


		A picture is worth a thousand words. In this spirit, you can use WEBKNOSSOS to create eye-catching animation of your datasets as a video clip. You can use these short movies as part of a presentation, website, for social media or to promote a publication.

		// animation video

		@@ -0,0 +1,19 @@
		# Animations

		A picture is worth a thousand words. In this spirit, you can use WEBKNOSSOS to create eye-catching animation of your datasets as a video clip. You can use these short movies as part of a presentation, website, for social media or to promote a publication.

	A picture is worth a thousand words. In this spirit, you can use WEBKNOSSOS to create eye-catching animation of your datasets as a video clip. You can use these short movies as part of a presentation, website, for social media or to promote a publication.
	A picture is worth more than a thousand words. In this spirit, you can use WEBKNOSSOS to create an eye-catching animation of your datasets as a video clip. You can use these short movies as part of a presentation, website, for social media or to promote a publication.


		WEBKNOSSOS can read [N5 datasets](https://github.com/saalfeldlab/n5).

		!!!info

Updated documentation #7439

Updated documentation #7439

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hotzenklotz commented Nov 14, 2023 • edited Loading

URL of deployed dev instance (used for testing):

Steps to test:

DO NOT MERGE WITHOUT WK_LIBS PR

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