slicereg

A 2D-3D histological brain slice registration application for mouse, rat, and zebrafish brains.

Features

At the moment, only some very basic features are implemented:

• Displays multi-channel OME-TIFF files onscreen.
• Loads 25um and 100um resolution Allen Mouse Reference Atlas into a 3D visualizer
• 2D slices can be translated and rotated in 3D space.

If you'd like to try it out, check the Installation section below.

Next Steps

Next features are focused on manual registration in the GUI:

• manual registration:
  • Comparison widget between section and reference atlas
  • Controls for full affine transforms
• multi-slice handling:
  • Load multiple slices at once
  • Slice selection and multi-slice manipulation interface.
• QuPath Visualization
  • Import QuPath files onto loaded slices for 3D visualization.
• More control over visualization
  • View manipulation tools (channel selector, atlas transparency controls, qupath show/hide, etc)
  • CLim controls

Installation

NOTE!!! If you are using MacOS BigSur OpenGL will not work. We are still waiting on a solution from other developers on how to fix this

Using Python

Downloading the source code

Get a copy of the project onto your computer using git:

git clone https://github.com/brainglobe/slicereg
cd slicereg

Setting up the Project

This project uses Poetry for installing dependencies; this is to make it easier for getting the same versions of python libraries on everyones' computer and help manage virtual environments. To get it, it can be pip-installed:

pip install poetry

To set up a virtual environment and install the dependencies (there are a lot of dependencies, this may take a couple minutes):

poetry install

Note: This project is python 3.8-only. If you get an error that says that python 3.8 is not available, then one way you can get it is with conda, if you have it installed already:

conda create -n py38 python=3.8
conda activate py38

Running the Project

Run the program:

poetry run bg-slicereg

Downloading Test Data

Some test data can be made available for project developers.
After you've been added to the access list, you can download it using DVC:

poetry run dvc pull

The first time you do this, there will be an authentication procedure.
It will ask you to go to a Google Drive link and log in.
Once you've logged in, copy-paste the authentication token from the browser into your terminal and press enter.
The example data will appear in the project's data directory.

Troubleshooting

"Virtual environment already activated:"

To solve this you will need to use pip to install the dependencies:

poetry export -f requirements.txt --dev --without-hashes --output requirements.txt
pip install -r requirements.txt

Display issues

In some cases (e.g. using WSL), you might need to export the display.

1. export DISPLAY=:0
2. run Xming

Data download

In case DVC pull is not working

ERROR: failed to pull data from the cloud - Checkout failed for following targets:

1. delete the folder cache in .dvc
2. rerun dvc pull