Tracing and analysis

This is the readme file accompanying the analysis pipeline for a anatomical tracing experiment.

General pipeline

1. image-preparation: Format and export images from proprietary file formats (e.g. .czi from Zeiss microscope) into general Tiffs format for aligning to reference atlas (AllenCCF) and/or cell counting.
2. alignment: Align each image or series of image to the reference atlas. Apply and store appropriate transformation.
3. cell-count: Mark cells or objects of interest on images. Either manually or via an algorithm. Input might be images of original or downsampled quality (to be determined).
4. summary: combining data from previous two steps (alignment and cell-count).

Dependency

• AP_histology requires "Curve Fitting Toolbox"
• AP_histology requires ColorBrewer/BrewerMap by DrosteEffect
• DeepSlice

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.

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 *Some additional resources at NiBabel and 3D Slicer. Basic directional:

• Left and Right
• Superior and Inferior
• Anterior and Posterior

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 Right is the positive direction. The same goes for A and S, which indicate that Anterior and Superior 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

• RAS
• origin: corner

Matlab 3D display

• XYZ with right-hand orientation.

Native Allen CCFv3

• PIR
• origin: corner

Cortex-lab processed Allen CCFv3