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Merge pull request #1681 from girder/improve-docs
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Add more commentary about bands and frames.
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manthey authored Oct 11, 2024
2 parents 1d4733c + 93eed8b commit 4c8dd55
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8 changes: 6 additions & 2 deletions docs/getting_started.rst
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Expand Up @@ -281,8 +281,8 @@ Any of the frames of such an image are accessed by adding a ``frame=<integer>``
format=large_image.constants.TILE_FORMAT_NUMPY)
# nparray will contain data from the middle channel image
Channels, Bands, Samples, and Axes
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Channels, Bands, Samples, Axes, and Frames
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Various large image formats refer to channels, bands, and samples. This isn't consistent across different libraries. In an attempt to harmonize the geospatial and medical image terminology, large_image uses ``bands`` or ``samples`` to refer to image plane components, such as red, green, blue, and alpha. For geospatial data this can often have additional bands, such as near infrared or panchromatic. ``channels`` are stored as separate frames and can be interpreted as different imaging modalities. For example, a fluorescence microscopy image might have DAPI, CY5, and A594 channels. A common color photograph file has 3 bands (also called samples) and 1 channel.

Expand All @@ -292,6 +292,10 @@ The ``z`` and ``t`` are common enough that they are sometimes considered as prim

Other axes are supported provided their names are case-insensitively unique.

Many image formats (such as TIFF) can contain multiple images within a single file. A single image within the file can have multiple bands. Channels, time series, and other axes are stored as separate images.

By default, the ``getTile``, ``getRegion``, and ``tileIterator`` methods will return all of the bands of a single frame. The specific bands returned can be modified using the ``style`` parameter. The specific frame, including any channel or other axes, is specified with the ``frame`` parameter.

Styles - Changing colors, scales, and other properties
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