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Navigate CCF by reference atlas - orientation and plate number #106

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carolth opened this issue Apr 23, 2020 · 1 comment
Open

Navigate CCF by reference atlas - orientation and plate number #106

carolth opened this issue Apr 23, 2020 · 1 comment
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Status: Triage Issues/PRs that need to be triaged

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@carolth
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carolth commented Apr 23, 2020

What's the problem this feature will solve?
Scientists who are processing tissues often consult a 2D atlas, and record their dissected areas based on an atlas plate (image in the series). When they go to record their dissection in Cell Locator, it would be useful to have an option to jump to an atlas plate. This is relevant for the Allen Mouse Brain Reference Atlas, and may also be implementable for the Allen Human Brain Reference Atlas. this could be referring to either a sagittal or coronal reference atlas plate.
Mouse static atlases: https://mouse.brain-map.org/static/atlas
Human static atlases: https://atlas.brain-map.org/atlas?atlas=138322605#atlas=138322605&plate=112360888&structure=10390&x=40320&y=46978.1328125&zoom=-7&resolution=124.49&z=3
Need to discuss which version of the static reference atlas plates to use for mouse (original or mirror image), and what plate numbers to use.

Describe the solution you'd like

Open Cell Locator. Somewhere there would be a toggle or option to select a reference atlas plate to open - select either the sagittal or the coronal atlas and enter plate number. CCF slice moves to the corresponding plane.

A BICCN collaborator dissects tissues and records the dissections on a sample of the reference atlas. She would want to open the tool and put in the reference atlas plate number to go to the correct plane and then draw her ROI.

Alternative Solutions

The work around is to try to navigate the CCF and find the correct section that aligns to the reference atlas - but if the reference atlas planes exist in Cell Locator, it would be much quicker.

Additional context

@carolth carolth added the Status: Triage Issues/PRs that need to be triaged label Apr 23, 2020
@wbwakeman
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I couldn't help myself from fooling around with this. For the coronal atlas, I think the following would get us pretty close to it.
for sections 1 to 132, replace "-10830.0" in the snippet of Cell Locator json below with a value according to the formula: -((sectionnumber-1)*100)+30
Thus, this snippet would be for section 109

    "DefaultSplineOrientation": [
        1.0,
        0.0,
        0.0,
        5686.5,
        0.0,
        0.0,
        1.0,
        -10830.0,
        0.0,
        1.0,
        0.0,
        -3987.5,
        0.0,
        0.0,
        0.0,
        1.0
    ],

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