Update readme.md

on coordinate systems

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.
+- 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