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Swain Lab
aliby
aliby-mirror
Commits
70ddf9f1
Commit
70ddf9f1
authored
2 years ago
by
Arin Wongprommoon
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docs: fix dimension order inconsistencies
REFERENCES: - issue #62
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04aea7e6
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docs/source/specifications/metadata.org
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docs/source/specifications/metadata.org
src/aliby/io/image.py
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src/aliby/io/image.py
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docs/source/specifications/metadata.org
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@@ -4,7 +4,7 @@ Draft for recommended metadata for images to provide a standard interface for al
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@@ -4,7 +4,7 @@ Draft for recommended metadata for images to provide a standard interface for al
* Essential data
* Essential data
- DimensionOrder: str
- DimensionOrder: str
Order of dimensions (e.g., TCZYX for Channel,
Time,
Z,Y,X)
Order of dimensions (e.g., TCZYX for
Time,
Channel, Z,
Y,
X)
- PixelSize: float
- PixelSize: float
Size of pixel, useful for segmentation.
Size of pixel, useful for segmentation.
- Channels: List[str]
- Channels: List[str]
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src/aliby/io/image.py
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@@ -5,7 +5,7 @@ Image: Loads images and registers them.
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@@ -5,7 +5,7 @@ Image: Loads images and registers them.
Image instances loads images from a specified directory into an object that
Image instances loads images from a specified directory into an object that
also contains image properties such as name and metadata. Pixels from images
also contains image properties such as name and metadata. Pixels from images
are stored in dask arrays; the standard way is to store them in 5-dimensional
are stored in dask arrays; the standard way is to store them in 5-dimensional
arrays: T(ime point), C(channel), Z(-stack),
X
,
Y
.
arrays: T(ime point), C(channel), Z(-stack),
Y
,
X
.
This module consists of a base Image class (BaseLocalImage). ImageLocalOME
This module consists of a base Image class (BaseLocalImage). ImageLocalOME
handles local OMERO images. ImageDir handles cases in which images are split
handles local OMERO images. ImageDir handles cases in which images are split
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