image2image-reg 0.3.0

Whole slide image registration using elastix.

image2image-reg

Whole slide image registration using elastix and/or Valis-WSI.

Overview

image2image-reg is a library for whole-slide image registration. It provides a command-line interface for performing registration, transformation and evaluation of whole-slide image registrations. The library is inspired by wsireg and valis. In fact, the registration workflow is a complete rewrite of the wsireg library to provide more flexibility and control over the registration process.

Differences from wsireg

• [DONE] Registrations are organized into projects. Project is a collection of configuration, logs, visualisations and images. This should provide a more structured way of organizing your images and not cluttering the working directory.
• [WIP] Registrations can be initialized with affine matrix (to get a good starting point) - this will allow for faster registration and hopefully better results.
• [WIP] Registrations can be focused on specific region of interest (mask) - while it's possible to do this in wsireg, it's not as straightforward as it should be.
• [DONE] Better support for point and GeoJSON data.
• [DONE] Better CLI interface - more structured and easier to use.
• [DONE] Better logging - more informative and easier to debug.
• [DONE] Reusable registrations - since all registration data is contained within the project, it's much easier to re-run certain tasks (such as export images) without having to re-run the registration process.

Planned features:

• [WIP] Better support for Valis registrations.
• [WIP] Better support for masks.
• Add better measures and means of testing effectiveness of registration.
• Add better multi-processing support.
• Add 3D module for elastiX registrations.

Getting started

The library provides a command-line interface which can be invoked:

i2reg --help

Will generate output like this:

Usage: i2reg [OPTIONS] COMMAND1 [ARGS]... [COMMAND2 [ARGS]...]...

  Launch registration app.

Options:
  --version      Show the version and exit.
  --dev          Flag to indicate that CLI should run in development mode and catch all errors.
  --no_color     Flag to disable colored logs (essential when logging to file).
  -q, --quiet    Minimal output - only errors and exceptions will be shown.
  --debug        Maximum output - all messages will be shown.
  -v, --verbose  Verbose output. This is additive flag so `-vvv` will print `INFO` messages and -vvvv will print
                 `DEBUG` information.
  --log FILE     Write logs to file (specify log path).
  -h, --help     Show this message and exit.

Project:
  new             Create a new project.
  about           Print information about the registration...
  validate        Validate project configuration.
  add-image       Add images to the project.
  add-path        Specify the registration path between the...
  add-attachment  Add attachment image to registered modality.
  add-points      Add attachment points (csv/tsv/txt) to...
  add-shape       Add attachment shape (GeoJSON) to...
  add-merge       Specify how (if) images should be merged.

Execute:
  preprocess  Preprocess images.
  register    Register images.
  clear       Clear project data...
  export      Export images.

Valis:
  valis-init      Initialize Valis configuration file.
  valis-register  Register images using the Valis algorithm.

Utility:
  merge    Export images.
  convert  Convert images to pyramidal OME-TIFF.

Contributing

Contributions are always welcome. Please feel free to submit PRs with new features, bug fixes, or documentation improvements.

git clone https://github.com/vandeplaslab/image2image-reg.git

pip install -e .[dev]