Category Archives: SPIM

ASCB15 part 1

The ASCB meeting brings scientists from all levels to talk about cell biology, which is actually almost anything “biology”. But there’s also a full program dedicated to other matters, like science careers, science publishing, science communications and science policy. This is also a great venue for companies to show their products, and for organizations/institutions to recruit new members. If I remember the numbers correctly, there were over 550 oral presentations and over 2,700 posters. I overheard someone saying there were ~6000 people attending the meeting. I typically go to RNA meetings that are mostly in the lower 100’s of participants. So, to me, that’s a large meeting.


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Open source microscope & software: openSPIM & Fiji

Just hears a great talk today by Pavel Tomancak from Max-Planck institute. He’s doing amazing work in systematic imaging of fly RNAome & proteome during development. Check out his website (click his name above).

He also talked about Fiji, which an open source software that is just like ImageJ, but with supporting community that develops new scripts & applications.

A most unusual “open source” development that he is very proud about is the openSPIM.

SPIM – Selective Plane Illumination Microscopy – is a microscopy method in which a laser beam sends a narrow light sheet to the specimen, and the objective is at 90 degree from the light sheet (there are SPIM developments with up to 4 objectives that can image from all 4 sides. See here). This type of microscopy is good for imaging thick live specimens (e.g. whole worm, fly or fish embryo etc..). Due to the thickness of the sample, wide field imaging will cause too much background.

So, there are good SPIM microscopes that you can buy from companies like Zeiss. but he developed the openSPIM, which is a build-it-yourself  SPIM microscope, that actually fits into a suitcase (he took it to South-Africa with him to show college & high-school kids). He claims that non-specialist can construct it in one hour. All the details (parts, assembly instructions (“IKEA/Lego style”) are found at the website. The cost, he estimates, is ~40,000$ (with the camera being about half the cost). He claims that the openSPIM is comparable, in quality of images, to commercial SPIM microscopes from 5 years ago.  Pretty good for standard imaging.

I like the idea.