Academic Commons Solution Stories

Tech Commoning Produces an Innovative, High-end Microscope

The following text is excerpted from a chapter by Jacques Paysan in the book Patterns of Commoning. The chapter describes an open source community of researchers and engineers that has created an innovative, high-end microscope called OpenSPIM.

 

The story suggests the great potential for open design and production of scientific instruments -- even quite sophisticated, complicated ones -- if researchers self-organize their collaboration as a commons. There is only a handful of companies in the world that otherwise manufacture such instruments, largely because the production of high-quality optical equipment in larger scales requires levels of precision and sophistication. However, global collaborations in open design and manufacturing are becoming more common, and extends to such diverse artifacts as motor vehicles, furniture, modular housing, and computer animation.

 

The full chapter, under a CC BY-SA license, can be found here: http://patternsofcommoning.org/openspim-a-high-tech-commons-for-research-and-education

 

Paysan writes:

 

SPIM is an acronym for “Selective Plane Illumination Microscopy,” which is also known by a more intuitive name, light-sheet microscopy. SPIM differs from other microscopic technologies in how it illuminates observed objects. In conventional instruments, the sample is usually illuminated along the optical axis, either through a lens underneath the object, or, through the microscope objective in the viewing direction. In light-sheet microscopy, however, the illumination light traverses the object like a thin sheet from one side to the other, perpendicular to the optical axis and not from below or above. This unusual configuration gave rise to the technology’s name – selective plane illumination.

 

SPIM can actually produce an “optical sectioning” enlargement of thick three-dimensional samples “on the fly.” …This process makes it possible to gently observe intact living samples for hours or even days and from multiple perspectives, without destroying the sample. Consequently, SPIM is typically used to observe insect larvae, zebrafish embryos, the growth of tumors, organoids, and regenerating nerve fibers. Because of its versatility, SPIM has quickly attracted a growing community of enthusiastic followers among researchers interested in non-invasive microscopy on living organisms….

 

“OpenSPIM started, once upon time, at the [Max Planck Institute for Molecular Cell Biology] canteen where they [researchers] dreamed up SPIM in a suitcase,” as Pavel Tomancak tweeted. “It actually exists!” Supported by the international Human Frontiers Scientific Program, the idea was first developed through a wiki, which, consistent with the basic ideas of the commons, was published under a Copyleft (CC BY-SA 3.0) license. In this wiki, the interested researcher can find a precise list of necessary parts, assembly instructions and video tutorials describing how to build a ready-to-use OpenSPIM instrument in less than one hour, in fourteen discrete steps. From the beginning, the OpenSPIM project committed itself to the principles of open hardware and open software….

 

To fully appreciate the achievements of this project, one needs to understand the complex and challenging data-analysis requirements of SPIM microscopy. Depending on its configuration, a SPIM microscope can generate more than 100 megabytes of data per second, potentially during the course of an entire week, all of which must be handled, stored, analyzed and rendered. Simply storing such vast quantities of data, where individual datasets can comprise up to several terabytes, is prohibitively costly for normal computing systems. The system often requires specific software that can work on cloud computing platforms, i.e. high-performance computing on distributed computer networks. Performing such computation at acceptable speeds on individual machines is highly problematic….

 

Whether OpenSPIM will continue to expand or simply remain an exciting niche project remains to be seen. This will substantially depend on whether or not the SPIM community – including the DIY builders and commercial providers – recognize the value of their ongoing commoning and perceive themselves as active commoners. Will they let their project modifications and improvements continue to flow back to the community and contribute to its flourishing?

 

If the OpenSPIM platform is seen simply as a launch pad for proprietary “secret projects” of either businesses or solitary nerds, it is quite possible the project will collapse. The community of OpenSPIM enthusiasts might at some point become exhausted by their voluntary efforts, and find it easier to retreat to their own private, proprietary interests. But there are reasons for optimism: In January 2015, the highly respected journal Nature Methods, which is affiliated with the prominent interdisciplinary scientific journal Nature, selected light-sheet microscopy as “Method of the Year 2014.”

 

Full essay can be found here: http://patternsofcommoning.org/openspim-a-high-tech-commons-for-research-and-education

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