A very short list of (bio)image formats, please 😊

[matuskalas]

Dear @tatianawoller @SebastianMunck @rabuono @glyg @joshmoore

I'd like to ask you all for a 2-minutes favour: Could you please each post a very short list of 4-8 (or max16) (bio)image formats you consider the most relevant in bioimaging in general?

I'd like to use it as the highest-priority list of formats that absolutely need to be in EDAM.

(Of course we have all the OME-* and the most generic ones like TIFF, JPEG, but we're missing the more specific ones)

Million thanks!!! 🙏🏽🙏🏽🙇🏽‍♂️

[glyg]

Hi @matuskalas the big vendors' formats (proprietary):

• metamorph .nd
• leica .lsm .lif (I think)
• zeiss .czi
• nikon .nd2

For open source, OME dominates I guess, with the addition of HDF5

Best :)
G

[joshmoore]

Hey @matuskalas! Thanks for the ping, but I'm going to dodge the question a bit. I would prefer to not by in the position of proposing my subjective "relevance". No objections with @glyg's list as he's chosen essentially by market share. I'll offer you another one -- imports into the IDR:

idr=> select value, count(value) from uploadjob_versioninfo where name = 'bioformats.reader' group by value order by count(value);
                value                |  count
-------------------------------------+---------
 loci.formats.in.FakeReader          |       1
 loci.formats.in.ICSReader           |       1
 loci.formats.in.GIFReader           |       2
 loci.formats.in.BDVReader           |       2
 loci.formats.in.MetamorphReader     |       3
 loci.formats.in.KLBReader           |       4
 loci.formats.in.PyramidTiffReader   |       7
 loci.formats.in.AVIReader           |      22
 loci.formats.in.SISReader           |      24
 loci.formats.in.LIFReader           |      62
 loci.formats.in.InCellReader        |     182
 loci.formats.in.ColumbusReader      |     208
 loci.formats.in.NDPIReader          |     348
 loci.formats.in.OperettaReader      |     419
 loci.formats.in.OIRReader           |     456
 loci.formats.in.PhotoshopTiffReader |     457
 loci.formats.in.ND2Reader           |     467
 loci.formats.in.CellWorxReader      |     471
 loci.formats.in.FlexReader          |     483
 loci.formats.in.SVSReader           |     558
 loci.formats.in.LeicaSCNReader      |     566
 loci.formats.in.ZeissZVIReader      |     600
 loci.formats.in.BDReader            |     676
 loci.formats.in.MicromanagerReader  |     828
 loci.formats.in.ZeissCZIReader      |     941
 loci.formats.in.FilePatternReader   |    1203
 loci.formats.in.CV7000Reader        |    1343
 loci.formats.in.JPEGReader          |    1428
 loci.formats.in.ScreenReader        |    1458
 loci.formats.in.ScanrReader         |    2016
 loci.formats.in.APNGReader          |    2301
 loci.formats.in.NRRDReader          |    3400
 loci.formats.in.ZeissLSMReader      |    3437
 loci.formats.in.DeltavisionReader   |    5125
 loci.formats.in.TiffDelegateReader  |   15303
 loci.formats.in.OMETiffReader       |  293257
 loci.formats.in.TiffReader          | 5931275
(37 rows)

As always, you can find more details about the specifics under https://j.mp/bio-formats-list

[rabuono]

Hey!

On the note of it being a rather biased list, here is one:

• PerkinElmer Operetta
• PerkinElmer Columbus
• Zeiss CZI
• Zeiss LSM (Laser Scanning Microscope) 510/710
• MRC (Medical Research Council)
• Leica LAS AF LIF (Leica Image File Format)
• IMOD
• Gatan Digital Micrograph
• Nikon NIS-Elements ND2

Names were copied from the bioformat list here

[SebastianMunck]

Hi all, I am focusing on those that have yet to be named. Here I would love to bring up the imaris file format, *.ims, Arivis *.sis, BigDattaViewer *.xml, hdf5 types, DICOM Image *.dcm DICOM Directory *.dicomdir, *.DICOMDIR (Dicom is an interesting one if you want to add it in the bioimage canon) Others that I believe have not been named but exceed the assignment of not listing too many Yokogawa CV *.mlf, Yokogawa CPf *.mmd, JPEG-2000 (*.jp2, *.j2k, *.j2c) Hamamatsu tiff-like file format (*.ndpi) High Dynamic Range Image (*.hdr) Abberior Imspector (.obf, .msr) Olympus file format (*.oir, *.oib, *.oif) Slidebook (.sld) Media Handler TrakEM2 Image file format (trakem2.xml, *.xml) Best Seb From: rafael buono ***@***.***> Sent: donderdag 2 november 2023 17:03 To: edamontology/edam-bioimaging ***@***.***> Cc: Sebastian Munck ***@***.***>; Mention ***@***.***> Subject: Re: [edamontology/edam-bioimaging] A very short list of (bio)image formats, please 😊 (Issue #34) Hey! On the note of it being a rather biased list, here is one: * PerkinElmer Operetta * PerkinElmer Columbus * Zeiss CZI * Zeiss LSM (Laser Scanning Microscope) 510/710 * MRC (Medical Research Council) * Leica LAS AF LIF (Leica Image File Format) * IMOD * Gatan Digital Micrograph * Nikon NIS-Elements ND2 Names were copied from the bioformat list here<https://bio-formats.readthedocs.io/en/stable/supported-formats.html> — Reply to this email directly, view it on GitHub<#34 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A5LW4YRPSFZER2DDG4RYZS3YCO7ZXAVCNFSM6AAAAAA62XRNQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJRGAZDCMZRHA>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#34 (comment)", "url": "#34 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

[tatianawoller]

Hi Matúš, From the perspective of my core facility, here are the most commonly used file format: - Nikon NIS-Element (.nd2) * Zeiss CZI (.czi) * Zeiss LSM (.lsm) * PerkinElmer Operetta (.tiff) * Dicom (.dcm) Kind regards, Tatiana From: Matúš Kalaš ***@***.***> Sent: 02 November 2023 12:37 To: edamontology/edam-bioimaging ***@***.***> Cc: Tatiana Woller ***@***.***>; Mention ***@***.***> Subject: [edamontology/edam-bioimaging] A very short list of (bio)image formats, please 😊 (Issue #34) Dear @tatianawoller<https://github.com/tatianawoller> @SebastianMunck<https://github.com/SebastianMunck> @rabuono<https://github.com/rabuono> @glyg<https://github.com/glyg> @joshmoore<https://github.com/joshmoore> I'd like to ask you all for a 2-minutes favour: Could you please each post a very short list of 4-8 (or max16) (bio)image formats you consider the most relevant in bioimaging in general? I'd like to use it as the highest-priority list of formats that absolutely need to be in EDAM. (Of course we have all the OME-* and the most generic ones like TIFF, JPEG, but we're missing the more specific ones) Million thanks!!! 🙏🏽🙏🏽🙇🏽‍♂️ — Reply to this email directly, view it on GitHub<#34>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AYSFXVD57DAK7EBOZPAKMS3YCOAWRAVCNFSM6AAAAAA62XRNQGVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3TIMBWGA3TENQ>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#34", "url": "#34", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]