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Error When Visualizing Local N5 File in Neuroglancer #602

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bang2003er opened this issue Jun 21, 2024 · 3 comments
Open

Error When Visualizing Local N5 File in Neuroglancer #602

bang2003er opened this issue Jun 21, 2024 · 3 comments

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@bang2003er
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bang2003er commented Jun 21, 2024

I followed the steps on this GitHub issue to visualize my local N5 file, but the final result looks like this (referring to the image). What could be the reason for this?
error

And this is my attributes.json

{
    "scales":[[
        128.0,
        128.0,
        128.0
    ]],
    "blockSize": [
        128,
        128,
        64
    ],
    "compression": {
        "level": -1,
        "type": "gzip",
        "useZlib": false
    },
    "dataType": "uint8",
    "dimensions": [
        1275,
        1185,
        1061
    ],
    "pixelResolution": {
        "dimensions": [
            128.0,
            128.0,
            128.0
        ],
        "unit": "nm"
    },
    "transform": {
        "axes": [
            "z",
            "y",
            "x"
        ],
        "order": "C",
        "scale": [
            128.0,
            128.0,
            128.0
        ],
        "translate": [
            60.0,
            60.0,
            60.0
        ],
        "units": [
            "nm",
            "nm",
            "nm"
        ]
    }
}


@xgui3783
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xgui3783 commented Jun 21, 2024

Try clicking "create as an image layer" at bottom right? (In yellow)

@bang2003er
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Try clicking "create as an image layer" at bottom right? (In yellow)

Thank you very much, I have successfully visualized the 3D structure. Does Neuroglancer provide a feature for high-resolution screenshots?

@jbms
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jbms commented Jun 28, 2024

You can do that using the Python module "neuroglancer.tool.screenshot" included in the Python package.

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3 participants