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Neural-Systems-at-UIO / LocaliZoom

Localizoom viewer https://localizoom.readthedocs.io
MIT License
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VisuAlign - Timm/thionin sections registered with non-linear anchoring (H201) #21

Closed blixilla closed 2 years ago

blixilla commented 3 years ago

I have a non-linear coordinate file that I would like to get a LocaliZoom-link for.

The coordinate file can be found on imb-neuroinf: Y:\hbp-02421_timm_thionine\0000_FINAL-Timm-Thionin\H201\QNII_anchoring\H201_TimmThionin_sagittal_US_new_VisuAlign_CHB_all.json

This corresponds to files in three blocks on N3: 841_2786_H201a, 841_2786_H201b and 841_2786_H201c

Tevemadar commented 3 years ago

Done, https://www.nesys.uio.no/NonLinTest/filmstripzoom.html?atlas=200100&series=4906,5253,5254 However some of the c-images seem to load much-much slower than the other two, like 069.

blixilla commented 3 years ago

Thank you for the link. Yes, it is really slow, and when it is done loading I see both atlas and markers, but the atlas is not adjusted according to the markers. Did you get that, as well?

blixilla commented 3 years ago

Hi again @Tevemadar ,

I was wondering if you could also create a link for the following Timm-series (H109) on imb-neuroinf: Y:\hbp-02421_timm_thionine\0000_FINAL-Timm-Thionin\H109\QNII_anchoring\H109_Timm_new_horizontal_VisuAlign_CHB_all.json

This corresponds to files in one block on N3: 841_4404_H109

Thanks in advance.

PS. I had some trouble aligning the atlas for some of the brain sections as I could only see a small part of neocortex. However, when I hovered over the rest of the section in VisuAlign, names of other brain regions popped up in colors below. Do you know what has happened here?

blixilla commented 3 years ago

Hi @Tevemadar , Unfortunately I made a mistake when asking you to create the LocaliZoom link for H201, directed you to the wrong blocks on N3 (the old versions, not the '_new'), sorry about this. The information below should be correct:

The coordinate file can be found on imb-neuroinf: Y:\hbp-02421_timm_thionine\0000_FINAL-Timm-Thionin\H201\QNII_anchoring\H201_TimmThionin_sagittal_US_new_VisuAlign_CHB_all.json

This corresponds to files in three blocks on N3: 841_2786_H201a_new, 841_2786_H201b_new and 841_2786_H201c_new

Would you be able to correct my mistake and create a new link?

Majpuc commented 3 years ago

@blixilla we will have to come back on this. Other priorities until M18 review

Majpuc commented 2 years ago

As this data will be uploaded to EBRAINS, new viewer links will be created. Issue closed 31.05.2022