BigStitcher: A Google Map For Tissues

  • Researchers built a new software program to make biological analysis easy. 
  • It processes large datasets automatically and enables interactive visualization, fast and precise alignment, and real-time fusion. 

Modern light microscopic methods — such as sample clearing and expansion microscopy — provide detailed insights into organs, but they generate enormous amounts of data that are extremely difficult to process.

These methods, with the help of advanced light-sheet microscopes, allow scientists to rapidly process large samples. However, such procedures produce excessive data (in terabytes), making it difficult for scientists to sift through and organize the data.

To create order in the chaos, a team of international researchers has built a software program named BigStitcher that makes the biological analysis process simple. It reconstructs the complex data in such a way that the outcome looks like a Google Map in 3D mode.

What Does It Do?

With BigStitcher, scientists can get an overview of the bigger picture: they can zoom in a specific position to analyze individual structures at the desired resolution.

More specifically, the software program enables interactive visualization, fast and precise alignment, real-time fusion, deconvolution and spatially resolved quality estimation of multitile, multiview datasets. It can double the size of specimens while compensating for optical effects and improving accuracy.

Reconstructing such large datasets with accuracy requires compensation for various types of images and intensity transformation that are introduced by the acquisition process. Therefore, the research team built an interactive stepwise process that compensates for all relevant transformation while providing spatially localized feedback on the quality of acquired data.

Reference: Nature Methods | DOI:10.1038/s41592-019-0501-0 | MDC

There is a zoom function that allows biologists to zoom in and visualize tiny details in high resolution. This could help them find answers to various questions. For example

  • Where exactly in the brain is cell division taking place?
  • Where do certain neuronal projections end?
  • Where is RNA expressed?

The program processes data automatically: it efficiently handles the management of large images, sparse datasets, quality estimation, and interactive fusion.

BigStitcher - Google Map For TissuesTwo virtual right-angled  cross-sections through the nervous system of a fruit fly larva 

BigStitcher outperforms existing software in terms of performance, functionality, and user interaction. It takes only tens of minutes to automatically reconstruct large datasets and supports cleared samples, conventional 2D and 3D confocal and wide-field acquisitions, as well as tiled multiview light-sheet acquisitions.

These features make BigStitcher a must-have tool for several laboratories. It is implemented in ImgLib and distributed within the Fiji framework.

Read: New Bioreactor Uses Tiny Pieces of Heart Tissue To Mimic Beating Heart

The best thing is the program doesn’t require intensive computation resources. You can run it on any standard computer and easily share data across your team members.

And since it’s an open-source tool, anyone can download it for free. The latest stable release is available on GitHub.

Written by
Varun Kumar

Varun Kumar is a professional science and technology journalist and a big fan of AI, machines, and space exploration. He received a Master's degree in computer science from Indraprastha University. To find out about his latest projects, feel free to directly email him at [email protected] 

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