https://github.com/lens-biophotonics/ZetaStitcher

ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
https://github.com/lens-biophotonics/ZetaStitcher

fluorescence-microscopy-imaging microscopy microscopy-images stitching volumetric-images

Last synced: 2 months ago
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ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

• Host: GitHub
• URL: https://github.com/lens-biophotonics/ZetaStitcher
• Owner: lens-biophotonics
• License: gpl-3.0
• Created: 2017-11-07T10:11:59.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2024-01-08T15:56:18.000Z (9 months ago)
• Last Synced: 2024-07-07T11:22:41.497Z (3 months ago)
• Topics: fluorescence-microscopy-imaging, microscopy, microscopy-images, stitching, volumetric-images
• Language: Python
• Homepage:
• Size: 3.15 MB
• Stars: 37
• Watchers: 6
• Forks: 6
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

Awesome Lists containing this project

• awesome-biological-image-analysis - ZetaStitcher - Tool designed to stitch large volumetric images such as those produced by light-sheet fluorescence microscopes. (Other)

README

        






ZetaStitcher is a tool designed to stitch large volumetric images such as

those produced by Light-Sheet Fluorescence Microscopes.

Key features:

* able to handle datasets as big as 1012 voxels

* multichannel images

* powerful and simple Python API to query arbitrary regions within the fused

volume

## How to install

On Ubuntu 20.04 LTS, run these commands:

```

sudo apt-get install python3-pip libgl1 libglib2.0-0

pip3 install zetastitcher

```

## Docker image

To build a docker image with ZetaStitcher:

```

make docker

```

You can call the stitching commands using an ephemeral container like this:

```

docker run -it -v`pwd`:/home --rm zetastitcher stitch-align -h

docker run -it -v`pwd`:/home --rm zetastitcher stitch-fuse -h

```

## Documentation

Please read the documentation and follow the tutorial at this page:


https://lens-biophotonics.github.io/ZetaStitcher/

## Acknowledgements

This open source software code was developed in whole in the Human

Brain Project, funded from the European Union’s Horizon 2020 Framework

Programme for Research and Innovation under Specific Grant Agreements

No. 720270 and No. 785907 (Human Brain Project SGA1 and SGA2).





Co-funded by the European Union