From 1ed86d58b2401c0a214dbbdf0c4d1b603ded67fb Mon Sep 17 00:00:00 2001 From: Aaron Benson Wong Date: Tue, 15 Oct 2024 16:57:34 +0200 Subject: [PATCH] Update readme.md on coordinate systems --- readme.md | 36 +++++++++++++++++++++++++++++++++++- 1 file changed, 35 insertions(+), 1 deletion(-) diff --git a/readme.md b/readme.md index 69761d9..e11a965 100644 --- a/readme.md +++ b/readme.md @@ -16,4 +16,38 @@ This is the readme file accompanying the analysis pipeline for a anatomical trac ## Installation of DeepSlice - Python 3.7 is needed (not later, e.g. 3.11 as of Nov 2023) - This can be done by installing miniconda or anaconda (search for installation file from archive) -- Then `pip install DeepSlice` should work. \ No newline at end of file +- Then `pip install DeepSlice` should work. + +# Notes on Coordinate Systems +There are a number of (standard) ways to represent a 3D volume in a data file or coordinate system. The convention varies across disciplines and different datasets. Two important pieces of information are: +1. how the 3 dimensions are ordered ("Voxel-Order"), and +2. which direction is defined as positive ("Orientation"). + +Additionally, some coordinate system uses a reference point not at the corner of the volume as origin (0,0,0), e.g. relative to Bregma. + +## Terminology +*This section is based on: [Orientation and Voxel-Order Terminology](http://www.grahamwideman.com/gw/brain/orientation/orientterms.htm)* +*Some additional resources at [NiBabel](https://nipy.org/nibabel/neuro_radio_conventions.html) and [3D Slicer](https://www.slicer.org/wiki/Coordinate_systems). +Basic directional: +- **L**eft and **R**ight +- **S**uperior and **I**nferior +- **A**nterior and **P**osterior + +A specification of RAS for example, illustrates that left-right is the first dimension, anterior-posterior is the second, and superior-inferior is the thrid. The R means that **R**ight is the positive direction. The same goes for A and S, which indicate that **A**nterior and **S**uperior are the positive directions of their respective axes. + +Left-hand and right-handed orientations refers to how the 3 ordered positive direction are related to each other. One can check it with the thumb-index-middle fingers of each hand. + +## Specification of relevant dataset/systems + +### The [QUINT workflow](https://quint-workflow.readthedocs.io/en/latest/) +- RAS +- origin: corner + +### Matlab 3D display +- XYZ with right-hand orientation. + +### Native Allen CCFv3 +- PIR +- origin: corner + +### Cortex-lab processed Allen CCFv3 \ No newline at end of file