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edamontology / edam-bioimaging

Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, and developed in an open collaboration including partners from NEUBIAS (neubias.org), COMULIS (comulis.eu), and ELIXIR (elixir-europe.org)..
https://webprotege.stanford.edu/#projects/2ce704bf-83ed-4d2e-985f-84c4841fac71/edit/Classes
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A very short list of (bio)image formats, please 😊 #34

Open matuskalas opened 1 year ago

matuskalas commented 1 year ago

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!!! πŸ™πŸ½πŸ™πŸ½πŸ™‡πŸ½β€β™‚οΈ

glyg commented 1 year ago

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

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

Best :) G

joshmoore commented 1 year ago

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 commented 1 year ago

Hey!

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

Names were copied from the bioformat list here

SebastianMunck commented 1 year ago

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:

Names were copied from the bioformat list herehttps://bio-formats.readthedocs.io/en/stable/supported-formats.html

β€” Reply to this email directly, view it on GitHubhttps://github.com/edamontology/edam-bioimaging/issues/34#issuecomment-1791021318, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A5LW4YRPSFZER2DDG4RYZS3YCO7ZXAVCNFSM6AAAAAA62XRNQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJRGAZDCMZRHA. You are receiving this because you were mentioned.Message ID: @.**@.>> [ { @.": "http://schema.org", @.": "EmailMessage", "potentialAction": { @.": "ViewAction", "target": "https://github.com/edamontology/edam-bioimaging/issues/34#issuecomment-1791021318", "url": "https://github.com/edamontology/edam-bioimaging/issues/34#issuecomment-1791021318", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { @.": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

tatianawoller commented 1 year ago

Hi MatΓΊΕ‘,

From the perspective of my core facility, here are the most commonly used file format: - Nikon NIS-Element (.nd2)

Kind regards,

Tatiana

From: Matúő Kalaő @.> 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 @tatianawollerhttps://github.com/tatianawoller @SebastianMunckhttps://github.com/SebastianMunck @rabuonohttps://github.com/rabuono @glyghttps://github.com/glyg @joshmoorehttps://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!!! πŸ™πŸ½πŸ™πŸ½πŸ™‡πŸ½β€β™‚οΈ

β€” Reply to this email directly, view it on GitHubhttps://github.com/edamontology/edam-bioimaging/issues/34, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYSFXVD57DAK7EBOZPAKMS3YCOAWRAVCNFSM6AAAAAA62XRNQGVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE3TIMBWGA3TENQ. You are receiving this because you were mentioned.Message ID: @.**@.>> [ { @.": "http://schema.org", @.": "EmailMessage", "potentialAction": { @.": "ViewAction", "target": "https://github.com/edamontology/edam-bioimaging/issues/34", "url": "https://github.com/edamontology/edam-bioimaging/issues/34", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { @.": "Organization", "name": "GitHub", "url": "https://github.com" } } ]