From 70ddf9f17c5d209a0d7abaa472fc05271f7512b8 Mon Sep 17 00:00:00 2001 From: arinwongprommoon <arin.wongprommoon@ed.ac.uk> Date: Mon, 23 Jan 2023 12:32:20 +0000 Subject: [PATCH] docs: fix dimension order inconsistencies REFERENCES: - issue #62 --- docs/source/specifications/metadata.org | 2 +- src/aliby/io/image.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/specifications/metadata.org b/docs/source/specifications/metadata.org index c7dc02b0..52d514a3 100644 --- a/docs/source/specifications/metadata.org +++ b/docs/source/specifications/metadata.org @@ -4,7 +4,7 @@ Draft for recommended metadata for images to provide a standard interface for al * Essential data - 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 Size of pixel, useful for segmentation. - Channels: List[str] diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py index 57283dc4..ca9daa64 100644 --- a/src/aliby/io/image.py +++ b/src/aliby/io/image.py @@ -5,7 +5,7 @@ Image: Loads images and registers them. Image instances loads images from a specified directory into an object that 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 -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 handles local OMERO images. ImageDir handles cases in which images are split -- GitLab