Open-source could finally get the world’s microscopes speaking the same language

Re:Open-source could finally get the world’s microscopes spe... by klysm on Monday October 02, 2023 @12:21PM (#37740288)

Microscope vendors have gone to incredible efforts to obfuscate their file formats. Some inventing custom compression codecs. I worked for a company that spent enormous amounts of time reverse engineering these protocols.

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Re:Open-source could finally get the world’s microscopes spe... by Ericson2314 on Monday October 02, 2023 @12:51PM (#37740855)

Labs should not be allowed to spend grant money on this bullshit.

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Re:Open-source could finally get the world’s microscopes spe... by ahns on Monday October 02, 2023 @12:55PM (#37740914)

:/ [tell me about it...](https://paulbourke.net/dataformats/svs/)

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Re:Open-source could finally get the world’s microscopes spe... by yread on Monday October 02, 2023 @02:13PM (#37742189)

Hah SVS is child's play compared to MRXS:

https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-...

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Re:Open-source could finally get the world’s microscopes spe... by extraduder_ire on Monday October 02, 2023 @06:55PM (#37745563)

I'd hope imagemagick or some other program can at least get the data out into another format. I did not know about openslide before reading that mail, but I'll try to keep it in mind.

Here's hoping this eventually gets fixed in a similar sort of way the .mkv format "fixed" video.

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Re:Open-source could finally get the world’s microscopes spe... by klysm on Monday October 02, 2023 @07:08PM (#37745673)

I wasn’t going to namedrop in my original comment but oh my the horrors this format brings back.

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Re:Open-source could finally get the world’s microscopes spe... by dekhn on Monday October 02, 2023 @01:15PM (#37741276)

bioformats2raw https://github.com/glencoesoftware/bioformats2raw handles a wide range of obfuscated formats.

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Re:Open-source could finally get the world’s microscopes spe... by m463 on Monday October 02, 2023 @01:16PM (#37741292)

I'm wondering if decent standards are created, we'll be able to buy an electron microscope on amazon, just like 3d printers.

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Re:Open-source could finally get the world’s microscopes spe... by jrockway on Monday October 02, 2023 @01:41PM (#37741709)

[delayed]

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Re:Open-source could finally get the world’s microscopes spe... by alted on Monday October 02, 2023 @01:56PM (#37741932)

I believe this is the Voxa Mochii [1].

[1] https://www.mymochii.com/

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Re:Open-source could finally get the world’s microscopes spe... by jrockway on Monday October 02, 2023 @02:06PM (#37742085)

Looks like it. Not quite as consumer grade as I expected; "contact us for a quote" = $$$.

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Re:Open-source could finally get the world’s microscopes spe... by jimmyswimmy on Monday October 02, 2023 @02:19PM (#37742270)

You'd want a quote if you're spending that kind of money: https://www.voxa.co/solutions/mochii/faqs

How much does one unit cost?

Mochii starts at $48K for the imaging only unit. The spectroscopy-enabled version, which provides full featured x-ray spectroscopy and spectrum imaging, is $65K.

It has an integrated metal coater option available for $5,000, and we offer a variety of optical cartridge exchange programs that can fit your consumables utilization and pricing needs.

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Re:Open-source could finally get the world’s microscopes spe... by jrockway on Monday October 02, 2023 @04:01PM (#37743675)

Yeah I kind of thought that if it was on YouTube then it was like $1000 or something. Apparently not.

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Re:Open-source could finally get the world’s microscopes spe... by dekhn on Monday October 02, 2023 @02:10PM (#37742137)

No. Also, this is a standard for light microscopy, not EM.

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Re:Open-source could finally get the world’s microscopes spe... by m463 on Monday October 02, 2023 @06:31PM (#37745336)

I guess a unified format is harder...

https://en.wikipedia.org/wiki/Optical_microscope#Alternative...

I was hoping for an easy entry:

https://www.hackster.io/michalin70/3d-printed-laser-scanning...

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Re:Open-source could finally get the world’s microscopes spe... by michaelmior on Monday October 02, 2023 @03:13PM (#37742978)

> Some inventing custom compression codecs.

I'm probably not being cynical enough here, but this doesn't necessarily imply a desire for obfuscation.

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Re:Open-source could finally get the world’s microscopes spe... by strangattractor on Monday October 02, 2023 @03:56PM (#37743599)

You are not being cynical enough - "Vendor lock in" would be a more appropriate term;)

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Re:Open-source could finally get the world’s microscopes spe... by eternityforest on Monday October 02, 2023 @05:49PM (#37744936)

A custom codec seems like it could only be obfuscation or really, really bad design.

Codecs are hard, I doubt there are many which are better than the well known ones.

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Re:Open-source could finally get the world’s microscopes spe... by michaelmior on Wednesday October 04, 2023 @02:57PM (#37769933)

When you're dealing with a specific subdomain, it's certainly possible you can exploit known properties of data in that domain to achieve better compression than a general purpose algorithm.

That said, it's certainly worthwhile benchmarking (de)compression speed and the compression ratio to see if the difference is actually meaningful enough to be worthwhile.

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