Help needed in tracing/ annotation

[sukeshsangam]

we are trying to annotate some datasets, but we are having trouble viewing skeletons in the data volumes of CATMAID. Specifically, once you switch z-layers, only the active node is shown: all other skeleton points (and adjoining edges) disappear.

For Example: When I start tracing from the Z layer 1, if I mark points(tracing ) on this layer and then move to z-layer 2 and come back to z-layer 1, I can't view my skeletons/ points which I have done before. When I switch back to z-layer 2 only the active node is shown.

Could somebody please help us with this issue, please let me know if I need to change any settings or what is the correct way of doing tracing in detail.

Thank you,
Sukesh.

[sukeshsangam]

@tomka Could you please help me with this.

[sukeshsangam]

Hey @aschampion, could you please help me with this.

[tomka]

Hi @sukeshsangam, what CATMAID version are you using (lower left corner status bar on front page)? Do you see errors or warnings displayed when switching layers? Also, it would be interesting to see if there are errors shown in the browser's dev tools. In Chrome/Chromium you can open the browser menu (upper right corner), select More Tools and there open Developer Tools. The Console tab might reveal some more information. The Network tab might help to see if particular requests fail.

[sukeshsangam]

Hi @tomka ,

This is the CATMAID version I am using, (CATMAID Version 2021.12.21-21-g9f3312f2e).

No errors and no new warnings displayed in the dev console.

When the initial load finished, I see below warnings,

three.js-lib.b69f140a3d93.js:4 THREE.TrackballControls: As part of the transition to ES6 Modules, the files in 'examples/js' were deprecated in May 2020 (r117) and will be deleted in December 2020 (r124). You can find more information about developing using ES6 Modules in https://threejs.org/docs/#manual/en/introduction/Installation.
(anonymous) @ three.js-lib.b69f140a3d93.js:4
three.js-lib.b69f140a3d93.js:7705 THREE.ExplodeModifier: As part of the transition to ES6 Modules, the files in 'examples/js' were deprecated in May 2020 (r117) and will be deleted in December 2020 (r124). You can find more information about developing using ES6 Modules in https://threejs.org/docs/#manual/en/introduction/Installation.
(anonymous) @ three.js-lib.b69f140a3d93.js:7705
DevTools failed to load source map: Could not load content for http://catmaid-url:8000/static/js/libs/jquery-2.1.3.min.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE
DevTools failed to load source map: Could not load content for http://catmaid-url:8000/static/js/libs/pixi.min.js.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE
DevTools failed to load source map: Could not load content for http://catmaid-url8000/static/js/libs/cola.js.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE
DevTools failed to load source map: Could not load content for http://catmaid-url:8000/static/js/libs/polyfill.min.js.map: HTTP error: status code 404, net::ERR_HTTP_RESPONSE_CODE_FAILURE
catmaid.282fe8ededd2.js:4448

But when I go to settings in dev console and uncheck "Enable Java Script Source maps". The above warning disappeared.

But the problem with tracing still exists.

Tracing in our setup is not displayed in the below way:

https://l1em.catmaid.virtualflybrain.org/?pid=1&zp=108250&yp=82961.59999999999&xp=54210.799999999996&tool=tracingtool&sid0=1&s0=2.4999999999999996&help=true&layout=h(XY,%20%7B%20type:%20%22neuron-search%22,%20id:%20%22neuron-search-1%22,%20options:%20%7B%22annotation-name%22:%20%22papers%22%7D%7D,%200.6)

few tracing data is displayed only when I check "Apply and show tracing window". I got this option when I click on left corner settings button, when i opened a CATMAID project.
In this settings, when i extend the tracing window and height to image length and height, few tracing data which was shown before is getting disappeared.

Could you please let us know, is there any additional settings need to be done to make it work as expected.

Thank you,
Sukesh.

[SanjaJasek]

Hi @sukeshsangam, we had a similar problem a while ago, it turned out that defining the z resolution as a float was causing it (see issue #606). Do you think it could be the same in your case?

[sukeshsangam]

Hi @SanjaJasek, We don't have the z resolution as float values, but when we enter the integer value as a resolution for the project, it automatically converting it to the float value. For example, for one of or project it has 10,10,10 as the resolution. When I enter this into the resolution field, it is converting it into the 10.0, 10.0, 10.0 . Does this causes the issue. Could you please let me know.

Thank you so much,
sukesh.

[sukeshsangam]

Hi @SanjaJasek ,

When we are talking about z resolution, is this the z resolution (the below screenshot) we were talking about it right?

And for creating the project in the CATMIAD, I used to this (https://github.com/catmaid/CATMAID/blob/master/scripts/tiles/tile_stack) script to create the mippyramids and hosted them on http wed server. Then I used the http web url of mippyramids to provide in the IMAGE BASE field which is shown in below field.

Is this process looks fine ?

And for tracing/annotations could you please explain or provide any resources which explains the complete workflow.

We are doubting our workflow in doing tracing/annotations.

Do we need to enable any configurations or setting in the web UI to avoid the issue(nodes getting disappeared)?

Thank you so much,
Sukesh.

[sukeshsangam]

Hello all,

The issue is resolved when I use the catmaid docker container from the docker hub.

Seems like when I am building the docker container from the source code on my server, few packages/libraries are missing. The docker built was always success without throwing any error.

Thank you so much,
Sukesh.