https://github.com/imcf/zeiss-lightsheet-bigstitcher

Fiji script for processing zeiss lightsheet datasets using BigStitcher
https://github.com/imcf/zeiss-lightsheet-bigstitcher

Last synced: about 2 months ago
JSON representation

Fiji script for processing zeiss lightsheet datasets using BigStitcher

• Host: GitHub
• URL: https://github.com/imcf/zeiss-lightsheet-bigstitcher
• Owner: imcf
• License: gpl-3.0
• Created: 2020-07-07T13:29:53.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2022-06-15T11:58:08.000Z (over 2 years ago)
• Last Synced: 2024-03-26T21:50:24.054Z (9 months ago)
• Language: Python
• Size: 345 KB
• Stars: 0
• Watchers: 6
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# Fiji scripts for processing Zeiss lightsheet Z.1/7 datasets using BigStitcher/ Multiview Reconstruction

These scripts are meant for automatic and easy "happy go lucky" processing of Zeiss Lightsheet datasets using the amazing [BigStitcher](https://imagej.net/BigStitcher) and [MultiView Reconstruction](https://imagej.net/Multiview-Reconstruction) in Fiji.

The goal is to provide a simple user interface to reduce the barrier of using the Lightsheet system for everyday users, for example in a facility environment. 

The scripts set default parameters that worked for several different usecases.

## Requirements

forked multiview-reconstruction-0.11.4-SNAPSHOT.jar which includes a Zeiss Lightsheet 7 reader (props to @lguerard)

https://github.com/imcf/multiview-reconstruction/releases/tag/0.11.4

If you would like to use the "convert to Imaris" function, 

- Imaris (Windows)

If you would like to use the mailing function,

- please change the smtp server settings according to your institute

## zeiss-lightsheet-bigstitcher

For stitching tiled datasets.

## zeiss-lightsheet-multiview-reconstruction.py

For reconstructing MultiView (=multi-angle) datasets