https://github.com/google-research/sofima

Scalable Optical Flow-based Image Montaging and Alignment
https://github.com/google-research/sofima

2d 3d 4d alignment-algorithm biomedical-image-processing connectomics electron-microscopy jax microscopy python3 stitching-algorithm

Last synced: 6 days ago
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Scalable Optical Flow-based Image Montaging and Alignment

• Host: GitHub
• URL: https://github.com/google-research/sofima
• Owner: google-research
• License: apache-2.0
• Created: 2022-02-11T11:49:48.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-12-09T23:36:20.000Z (13 days ago)
• Last Synced: 2024-12-10T00:26:59.321Z (12 days ago)
• Topics: 2d, 3d, 4d, alignment-algorithm, biomedical-image-processing, connectomics, electron-microscopy, jax, microscopy, python3, stitching-algorithm
• Language: Jupyter Notebook
• Homepage:
• Size: 4.72 MB
• Stars: 54
• Watchers: 8
• Forks: 13
• Open Issues: 9
• Metadata Files:
  • Readme: README.md
  • Contributing: docs/contributing.md
  • License: LICENSE

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README

        
# SOFIMA

SOFIMA (Scalable Optical Flow-based Image Montaging and Alignment) is a tool

for stitching, aligning and warping large 2d, 3d and 4d microscopy datasets.

[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

This is not an officially supported Google product.

# Installation

SOFIMA is implemented purely in Python, and does not require a build step. To

install it directly from the repository, run:

```shell

  pip install git+https://github.com/google-research/sofima

```

# Overview

SOFIMA uses optical flow regularized with an elastic mesh to establish

maps between data in different coordinate systems. Both the [flow estimator](flow_field.py)

as well as the [mesh solver](mesh.py) are implemented in [JAX](https://github.com/google/jax)

and will automatically take advantage of GPU acceleration if the hardware if available.

A core data structure used throughout the project is a *coordinate map* stored

as a dense array of relative offsets (see the module docstring in [map_utils.py](map_utils.py)

for details). Among other uses, this is the representation of the estimated flow fields

and the mesh node positions.

# Example usage

 * [electron microscopy tile stitching](https://colab.research.google.com/github/google-research/sofima/blob/main/notebooks/em_stitching.ipynb)

 * [electron microscopy section alignment](https://colab.research.google.com/github/google-research/sofima/blob/main/notebooks/em_alignment.ipynb)

# License

Licensed under the Apache License, Version 2.0 (the "License");

you may not use this software except in compliance with the License.

You may obtain a copy of the License at .

Unless required by applicable law or agreed to in writing, software

distributed under the License is distributed on an "AS IS" BASIS,

WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

See the License for the specific language governing permissions and

limitations under the License.