Treffer: From cells to pixels: A decision tree for designing bioimage analysis pipelines.
Title:
From cells to pixels: A decision tree for designing bioimage analysis pipelines.
Authors:
Fazeli E; Biomedicum Imaging Unit, Faculty of Medicine and HiLIFE, University of Helsinki, Helsinki, Finland., Haase R; Data Science Center, Leipzig University, Leipzig, Germany.; Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Dresden, Leipzig, Germany., Doube M; Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China., Miura K; Bioimage Analysis & Research, Okayama, Japan.; Graduate School of Frontier Biosciences, The University of Osaka, Osaka, Japan., Legland D; UR BIA, INRAE, Nantes, France.; PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes, France.
Source:
Journal of microscopy [J Microsc] 2025 Dec; Vol. 300 (3), pp. 384-408. Date of Electronic Publication: 2025 Aug 29.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Published for the Royal Microscopical Society by Blackwell Scientific Publications Country of Publication: England NLM ID: 0204522 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-2818 (Electronic) Linking ISSN: 00222720 NLM ISO Abbreviation: J Microsc Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford, Published for the Royal Microscopical Society by Blackwell Scientific Publications.
MeSH Terms:
References:
Plant Physiol. 2012 Mar;158(3):1230-40. (PMID: 22247269)
J Neurosci Methods. 2006 Mar 15;151(2):168-77. (PMID: 16157388)
J Microsc. 2003 Jan;209(Pt 1):34-40. (PMID: 12535182)
J Microsc. 2005 Dec;220(Pt 3):131-9. (PMID: 16363997)
F1000Res. 2020 Oct 28;9:1279. (PMID: 33224481)
Nat Commun. 2022 Dec 3;13(1):7480. (PMID: 36463283)
Methods. 2017 Feb 15;115:80-90. (PMID: 27713081)
PLoS One. 2013 Dec 04;8(12):e80914. (PMID: 24349021)
Nat Methods. 2015 Nov;12(11):1065-71. (PMID: 26344046)
J Comp Neurol. 2009 Apr 10;513(5):483-95. (PMID: 19226531)
J Appl Physiol (1985). 2019 Mar 1;126(3):638-646. (PMID: 30629475)
Mycorrhiza. 2020 May;30(2-3):229-242. (PMID: 32300867)
J Hered. 2002 Sep-Oct;93(5):384-5. (PMID: 12547931)
Methods Mol Biol. 2019;1992:291-305. (PMID: 31148046)
PLoS One. 2016 Oct 19;11(10):e0163915. (PMID: 27760153)
Front Cell Dev Biol. 2025 May 15;13:1572212. (PMID: 40443732)
Nat Biotechnol. 2016 Dec 7;34(12):1250-1255. (PMID: 27926723)
J Microsc. 2024 Jul;295(1):61-82. (PMID: 37269048)
J Microsc. 2004 Feb;213(2):158-71. (PMID: 14731299)
PLoS Pathog. 2024 May 28;20(5):e1011903. (PMID: 38805551)
J Microsc. 1999 Aug;195(Pt 2):96-103. (PMID: 10460672)
Adv Healthc Mater. 2022 May;11(9):e2102087. (PMID: 35137550)
J Appl Physiol (1985). 2006 Sep;101(3):926-33. (PMID: 16741256)
Life Sci Alliance. 2021 Jan 27;4(3):. (PMID: 33504622)
Nat Methods. 2023 Mar;20(3):424-431. (PMID: 36864197)
PLoS One. 2014 Mar 12;9(3):e90673. (PMID: 24622152)
J Neurosci Methods. 2014 Mar 30;225:65-70. (PMID: 24485871)
PLoS Comput Biol. 2009 Jun;5(6):e1000368. (PMID: 19557124)
Cell. 2013 Jan 31;152(3):479-91. (PMID: 23374344)
Plant Methods. 2018 Jul 04;14:52. (PMID: 29997681)
Comput Struct Biotechnol J. 2020 Jun 03;18:1287-1300. (PMID: 32612752)
PLoS One. 2014 Sep 24;9(9):e108255. (PMID: 25251072)
PLoS One. 2013 Jul 29;8(7):e70221. (PMID: 23922958)
Nat Methods. 2019 Dec;16(12):1247-1253. (PMID: 31636459)
J Microsc. 2024 Aug;295(2):93-101. (PMID: 38532662)
J Exp Bot. 2015 Mar;66(5):1387-95. (PMID: 25540436)
Nature. 2021 Aug;596(7871):211-220. (PMID: 34381231)
J Microsc. 2007 Aug;227(Pt 2):140-56. (PMID: 17845709)
Plant Cell. 2004 Oct;16(10):2546-52. (PMID: 15466408)
BMC Plant Biol. 2015 Oct 30;15:264. (PMID: 26518365)
Plant Physiol. 2007 Oct;145(2):305-16. (PMID: 17720760)
Nat Methods. 2012 Mar 04;9(4):410-7. (PMID: 22388289)
IEEE Trans Pattern Anal Mach Intell. 2013 Mar;35(3):568-81. (PMID: 22665719)
J Cell Biol. 2017 Oct 2;216(10):3405-3422. (PMID: 28760769)
Clin Radiol. 2004 Dec;59(12):1061-9. (PMID: 15556588)
Sci Rep. 2018 Feb 12;8(1):2826. (PMID: 29434299)
J Leukoc Biol. 2007 Jan;81(1):263-71. (PMID: 17046968)
Sci Rep. 2019 Apr 15;9(1):6084. (PMID: 30988411)
Adv Anat Embryol Cell Biol. 2016;219:69-93. (PMID: 27207363)
PLoS One. 2017 Apr 18;12(4):e0176103. (PMID: 28419171)
PLoS One. 2021 Dec 02;16(12):e0260509. (PMID: 34855812)
Nucleus. 2022 Dec;13(1):277-299. (PMID: 36447428)
Front Plant Sci. 2015 Sep 01;6:679. (PMID: 26388883)
Invest Ophthalmol Vis Sci. 2016 Jul 1;57(9):OCT362-70. (PMID: 27409494)
Nat Methods. 2023 Jul;20(7):976-978. (PMID: 37434006)
Front Cell Dev Biol. 2023 Sep 15;11:1267822. (PMID: 37779894)
Development. 2023 Feb 15;150(3):. (PMID: 36625162)
Cell Rep Methods. 2022 Nov 21;2(11):100348. (PMID: 36452868)
Cell Motil Cytoskeleton. 2009 Mar;66(3):156-65. (PMID: 19206151)
Elife. 2022 Oct 12;11:. (PMID: 36222498)
J Cell Sci Suppl. 1987;8:81-102. (PMID: 3503898)
Calcif Tissue Int. 2021 Sep;109(3):303-328. (PMID: 34086084)
Front Plant Sci. 2022 Feb 10;12:808365. (PMID: 35222454)
Mol Biol Cell. 2024 Dec 1;35(12):ar146. (PMID: 39441713)
J Biomech. 2014 Sep 22;47(12):3135-42. (PMID: 25065731)
Curr Eye Res. 2002 Apr;24(4):274-80. (PMID: 12324866)
Plant Methods. 2022 Dec 1;18(1):127. (PMID: 36457133)
PLoS Biol. 2016 Jan 04;14(1):e1002340. (PMID: 26727152)
J Microsc. 2017 Jan;265(1):101-110. (PMID: 27546192)
New Phytol. 2011 Sep;191(4):1168-1179. (PMID: 21569032)
Med Image Anal. 2016 Aug;32:18-31. (PMID: 27037463)
Development. 2016 Sep 15;143(18):3417-28. (PMID: 27387872)
PLoS One. 2010 Jul 22;5(7):e11631. (PMID: 20661478)
Nat Methods. 2012 Jun 28;9(7):697-710. (PMID: 22743775)
PLoS One. 2021 Aug 11;16(8):e0255835. (PMID: 34379652)
Traffic. 2022 May;23(5):238-269. (PMID: 35343629)
Science. 2022 Nov 18;378(6621):762-768. (PMID: 36395221)
Elife. 2023 Feb 16;12:. (PMID: 36795088)
PLoS Genet. 2010 Feb 12;6(2):e1000846. (PMID: 20174442)
Chromosome Res. 2008;16(3):523-62. (PMID: 18461488)
Adv Biochem Eng Biotechnol. 2005;95:267-95. (PMID: 16080272)
F1000Res. 2021 Apr 30;10:334. (PMID: 34164115)
Biophys J. 2023 Aug 8;122(15):3191-3205. (PMID: 37401053)
Comput Struct Biotechnol J. 2021 Apr 15;19:2106-2120. (PMID: 33995906)
Sci Rep. 2019 Mar 7;9(1):3794. (PMID: 30846705)
Prog Retin Eye Res. 2006 Jan;25(1):99-127. (PMID: 16154379)
PLoS Comput Biol. 2023 Aug 30;19(8):e1011407. (PMID: 37647341)
Foods. 2020 May 09;9(5):. (PMID: 32397405)
J Microsc. 2015 Jan;257(1):65-85. (PMID: 25233873)
Comput Biol Med. 2007 Mar;37(3):364-75. (PMID: 16793033)
Bone. 1997 Apr;20(4):315-28. (PMID: 9108351)
Front Physiol. 2021 Dec 08;12:755468. (PMID: 34955878)
New Phytol. 2022 May;234(3):946-960. (PMID: 35037256)
Methods Mol Biol. 2017;1563:185-207. (PMID: 28324610)
Sci Rep. 2020 Oct 29;10(1):18624. (PMID: 33122646)
Behav Res Methods Instrum Comput. 2000 Feb;32(1):63-71. (PMID: 10758665)
Methods Cell Biol. 2007;83:237-68. (PMID: 17613311)
J Microsc. 2024 Jun;294(3):338-349. (PMID: 37199456)
Front Cell Dev Biol. 2021 Nov 01;9:739079. (PMID: 34858975)
PLoS One. 2020 Sep 14;15(9):e0238926. (PMID: 32925940)
Mol Biol Cell. 2016 Jun 15;27(12):1948-57. (PMID: 27099372)
PLoS One. 2014 Sep 11;9(9):e107088. (PMID: 25210770)
BMC Bioinformatics. 2019 Jun 28;20(1):360. (PMID: 31253078)
Biophys J. 1991 Oct;60(4):910-21. (PMID: 1742458)
Sci Rep. 2017 Jun 7;7(1):2999. (PMID: 28592874)
Ann Anat. 2014 Jan;196(1):20-5. (PMID: 23773475)
PLoS One. 2017 Jun 29;12(6):e0180400. (PMID: 28662210)
Med Image Anal. 2012 May;16(4):904-14. (PMID: 22377657)
Annu Rev Biophys. 2023 May 9;52:139-160. (PMID: 37159293)
Elife. 2022 Nov 29;11:. (PMID: 36444654)
Nat Commun. 2021 Apr 15;12(1):2276. (PMID: 33859193)
Elife. 2015 Feb 12;4:. (PMID: 25675087)
Cell. 2021 Sep 2;184(18):4819-4837.e22. (PMID: 34380046)
Sci Rep. 2021 Jan 11;11(1):323. (PMID: 33431919)
Nat Methods. 2021 Dec;18(12):1427-1440. (PMID: 34862501)
Comput Struct Biotechnol J. 2023 Mar 09;21:2018-2034. (PMID: 36968017)
PLoS One. 2021 Apr 16;16(4):e0250093. (PMID: 33861785)
PLoS Comput Biol. 2010 Jul 08;6(7):e1000853. (PMID: 20628576)
Biomaterials. 1999 Dec;20(23-24):2235-44. (PMID: 10614930)
BMC Bioinformatics. 2012;13 Suppl 16:S11. (PMID: 23176142)
J Struct Biol. 2005 Aug;151(2):182-95. (PMID: 16043363)
J Microsc. 2025 Dec;300(3):384-408. (PMID: 40879663)
Biophys J. 2003 Aug;85(2):1289-306. (PMID: 12885672)
Nat Commun. 2023 May 9;14(1):2681. (PMID: 37160944)
Mol Biol Cell. 2016 Nov 7;27(22):3616-3626. (PMID: 27535428)
Sci Rep. 2018 Sep 12;8(1):13658. (PMID: 30209281)
Ann Bot. 2014 Sep;114(4):829-40. (PMID: 24989783)
Am J Physiol Cell Physiol. 2011 Apr;300(4):C723-42. (PMID: 21209361)
J Cell Biol. 2014 Jan 20;204(2):231-45. (PMID: 24446482)
F1000Res. 2021 Apr 26;10:320. (PMID: 34136134)
Nat Rev Methods Primers. 2021;1:. (PMID: 35663461)
BMC Biol. 2022 Aug 11;20(1):178. (PMID: 35953853)
Patterns (N Y). 2020 Jun 12;1(3):100038. (PMID: 33205106)
Traffic. 2017 Jan;18(1):71-88. (PMID: 27770501)
Mol Biol Cell. 2023 May 15;34(6):ar50. (PMID: 36515991)
Nat Methods. 2021 Dec;18(12):1418-1422. (PMID: 34021280)
J Cell Biol. 2023 Feb 6;222(2):. (PMID: 36534166)
PLoS One. 2014 Jan 23;9(1):e86646. (PMID: 24466185)
Nat Methods. 2010 Jul;7(7):547-53. (PMID: 20543845)
Sci Rep. 2022 Jan 7;12(1):167. (PMID: 34997100)
Nat Commun. 2023 Apr 3;14(1):1854. (PMID: 37012230)
Wellcome Open Res. 2021 Feb 22;6:37. (PMID: 33954267)
J Microsc. 2006 Dec;224(Pt 3):213-32. (PMID: 17210054)
Plants (Basel). 2023 Feb 24;12(5):. (PMID: 36903900)
Comput Methods Programs Biomed. 2022 Dec;227:107211. (PMID: 36356384)
Prostate. 2007 Feb 15;67(3):248-54. (PMID: 17075809)
PLoS One. 2022 Nov 18;17(11):e0276972. (PMID: 36399435)
PLoS One. 2011;6(11):e27385. (PMID: 22110636)
FASEB J. 2021 May;35(5):e21582. (PMID: 33835502)
Elife. 2019 Aug 13;8:. (PMID: 31405451)
Biophys J. 2006 Feb 15;90(4):1439-52. (PMID: 16326902)
FEBS Lett. 2022 Oct;596(19):2472-2485. (PMID: 35833863)
Med Image Anal. 2019 Aug;56:44-67. (PMID: 31181343)
Am J Physiol Endocrinol Metab. 2020 Feb 1;318(2):E87-E101. (PMID: 31846372)
Front Physiol. 2022 Jan 28;13:832417. (PMID: 35153840)
Front Cell Dev Biol. 2022 Sep 30;10:898351. (PMID: 36247011)
J Microsc. 1990 Feb;157(Pt 2):149-62. (PMID: 2313683)
Biophys J. 2011 Jun 8;100(11):2820-8. (PMID: 21641328)
Plant J. 2016 Nov;88(3):468-475. (PMID: 27354251)
Cytometry A. 2011 Jul;79(7):545-59. (PMID: 21674772)
Nat Methods. 2023 Apr;20(4):569-579. (PMID: 36997816)
J Theor Biol. 2007 Feb 21;244(4):597-620. (PMID: 17074362)
J Anat. 1953 Oct;87(4):387-406. (PMID: 13117757)
IEEE Rev Biomed Eng. 2016;9:234-63. (PMID: 26742143)
Nat Methods. 2022 Jul;19(7):829-832. (PMID: 35654950)
PLoS One. 2016 Aug 09;11(8):e0160735. (PMID: 27505420)
Science. 2017 Apr 14;356(6334):186-189. (PMID: 28408602)
J Neurosci Methods. 2006 Mar 15;151(2):168-77. (PMID: 16157388)
J Microsc. 2003 Jan;209(Pt 1):34-40. (PMID: 12535182)
J Microsc. 2005 Dec;220(Pt 3):131-9. (PMID: 16363997)
F1000Res. 2020 Oct 28;9:1279. (PMID: 33224481)
Nat Commun. 2022 Dec 3;13(1):7480. (PMID: 36463283)
Methods. 2017 Feb 15;115:80-90. (PMID: 27713081)
PLoS One. 2013 Dec 04;8(12):e80914. (PMID: 24349021)
Nat Methods. 2015 Nov;12(11):1065-71. (PMID: 26344046)
J Comp Neurol. 2009 Apr 10;513(5):483-95. (PMID: 19226531)
J Appl Physiol (1985). 2019 Mar 1;126(3):638-646. (PMID: 30629475)
Mycorrhiza. 2020 May;30(2-3):229-242. (PMID: 32300867)
J Hered. 2002 Sep-Oct;93(5):384-5. (PMID: 12547931)
Methods Mol Biol. 2019;1992:291-305. (PMID: 31148046)
PLoS One. 2016 Oct 19;11(10):e0163915. (PMID: 27760153)
Front Cell Dev Biol. 2025 May 15;13:1572212. (PMID: 40443732)
Nat Biotechnol. 2016 Dec 7;34(12):1250-1255. (PMID: 27926723)
J Microsc. 2024 Jul;295(1):61-82. (PMID: 37269048)
J Microsc. 2004 Feb;213(2):158-71. (PMID: 14731299)
PLoS Pathog. 2024 May 28;20(5):e1011903. (PMID: 38805551)
J Microsc. 1999 Aug;195(Pt 2):96-103. (PMID: 10460672)
Adv Healthc Mater. 2022 May;11(9):e2102087. (PMID: 35137550)
J Appl Physiol (1985). 2006 Sep;101(3):926-33. (PMID: 16741256)
Life Sci Alliance. 2021 Jan 27;4(3):. (PMID: 33504622)
Nat Methods. 2023 Mar;20(3):424-431. (PMID: 36864197)
PLoS One. 2014 Mar 12;9(3):e90673. (PMID: 24622152)
J Neurosci Methods. 2014 Mar 30;225:65-70. (PMID: 24485871)
PLoS Comput Biol. 2009 Jun;5(6):e1000368. (PMID: 19557124)
Cell. 2013 Jan 31;152(3):479-91. (PMID: 23374344)
Plant Methods. 2018 Jul 04;14:52. (PMID: 29997681)
Comput Struct Biotechnol J. 2020 Jun 03;18:1287-1300. (PMID: 32612752)
PLoS One. 2014 Sep 24;9(9):e108255. (PMID: 25251072)
PLoS One. 2013 Jul 29;8(7):e70221. (PMID: 23922958)
Nat Methods. 2019 Dec;16(12):1247-1253. (PMID: 31636459)
J Microsc. 2024 Aug;295(2):93-101. (PMID: 38532662)
J Exp Bot. 2015 Mar;66(5):1387-95. (PMID: 25540436)
Nature. 2021 Aug;596(7871):211-220. (PMID: 34381231)
J Microsc. 2007 Aug;227(Pt 2):140-56. (PMID: 17845709)
Plant Cell. 2004 Oct;16(10):2546-52. (PMID: 15466408)
BMC Plant Biol. 2015 Oct 30;15:264. (PMID: 26518365)
Plant Physiol. 2007 Oct;145(2):305-16. (PMID: 17720760)
Nat Methods. 2012 Mar 04;9(4):410-7. (PMID: 22388289)
IEEE Trans Pattern Anal Mach Intell. 2013 Mar;35(3):568-81. (PMID: 22665719)
J Cell Biol. 2017 Oct 2;216(10):3405-3422. (PMID: 28760769)
Clin Radiol. 2004 Dec;59(12):1061-9. (PMID: 15556588)
Sci Rep. 2018 Feb 12;8(1):2826. (PMID: 29434299)
J Leukoc Biol. 2007 Jan;81(1):263-71. (PMID: 17046968)
Sci Rep. 2019 Apr 15;9(1):6084. (PMID: 30988411)
Adv Anat Embryol Cell Biol. 2016;219:69-93. (PMID: 27207363)
PLoS One. 2017 Apr 18;12(4):e0176103. (PMID: 28419171)
PLoS One. 2021 Dec 02;16(12):e0260509. (PMID: 34855812)
Nucleus. 2022 Dec;13(1):277-299. (PMID: 36447428)
Front Plant Sci. 2015 Sep 01;6:679. (PMID: 26388883)
Invest Ophthalmol Vis Sci. 2016 Jul 1;57(9):OCT362-70. (PMID: 27409494)
Nat Methods. 2023 Jul;20(7):976-978. (PMID: 37434006)
Front Cell Dev Biol. 2023 Sep 15;11:1267822. (PMID: 37779894)
Development. 2023 Feb 15;150(3):. (PMID: 36625162)
Cell Rep Methods. 2022 Nov 21;2(11):100348. (PMID: 36452868)
Cell Motil Cytoskeleton. 2009 Mar;66(3):156-65. (PMID: 19206151)
Elife. 2022 Oct 12;11:. (PMID: 36222498)
J Cell Sci Suppl. 1987;8:81-102. (PMID: 3503898)
Calcif Tissue Int. 2021 Sep;109(3):303-328. (PMID: 34086084)
Front Plant Sci. 2022 Feb 10;12:808365. (PMID: 35222454)
Mol Biol Cell. 2024 Dec 1;35(12):ar146. (PMID: 39441713)
J Biomech. 2014 Sep 22;47(12):3135-42. (PMID: 25065731)
Curr Eye Res. 2002 Apr;24(4):274-80. (PMID: 12324866)
Plant Methods. 2022 Dec 1;18(1):127. (PMID: 36457133)
PLoS Biol. 2016 Jan 04;14(1):e1002340. (PMID: 26727152)
J Microsc. 2017 Jan;265(1):101-110. (PMID: 27546192)
New Phytol. 2011 Sep;191(4):1168-1179. (PMID: 21569032)
Med Image Anal. 2016 Aug;32:18-31. (PMID: 27037463)
Development. 2016 Sep 15;143(18):3417-28. (PMID: 27387872)
PLoS One. 2010 Jul 22;5(7):e11631. (PMID: 20661478)
Nat Methods. 2012 Jun 28;9(7):697-710. (PMID: 22743775)
PLoS One. 2021 Aug 11;16(8):e0255835. (PMID: 34379652)
Traffic. 2022 May;23(5):238-269. (PMID: 35343629)
Science. 2022 Nov 18;378(6621):762-768. (PMID: 36395221)
Elife. 2023 Feb 16;12:. (PMID: 36795088)
PLoS Genet. 2010 Feb 12;6(2):e1000846. (PMID: 20174442)
Chromosome Res. 2008;16(3):523-62. (PMID: 18461488)
Adv Biochem Eng Biotechnol. 2005;95:267-95. (PMID: 16080272)
F1000Res. 2021 Apr 30;10:334. (PMID: 34164115)
Biophys J. 2023 Aug 8;122(15):3191-3205. (PMID: 37401053)
Comput Struct Biotechnol J. 2021 Apr 15;19:2106-2120. (PMID: 33995906)
Sci Rep. 2019 Mar 7;9(1):3794. (PMID: 30846705)
Prog Retin Eye Res. 2006 Jan;25(1):99-127. (PMID: 16154379)
PLoS Comput Biol. 2023 Aug 30;19(8):e1011407. (PMID: 37647341)
Foods. 2020 May 09;9(5):. (PMID: 32397405)
J Microsc. 2015 Jan;257(1):65-85. (PMID: 25233873)
Comput Biol Med. 2007 Mar;37(3):364-75. (PMID: 16793033)
Bone. 1997 Apr;20(4):315-28. (PMID: 9108351)
Front Physiol. 2021 Dec 08;12:755468. (PMID: 34955878)
New Phytol. 2022 May;234(3):946-960. (PMID: 35037256)
Methods Mol Biol. 2017;1563:185-207. (PMID: 28324610)
Sci Rep. 2020 Oct 29;10(1):18624. (PMID: 33122646)
Behav Res Methods Instrum Comput. 2000 Feb;32(1):63-71. (PMID: 10758665)
Methods Cell Biol. 2007;83:237-68. (PMID: 17613311)
J Microsc. 2024 Jun;294(3):338-349. (PMID: 37199456)
Front Cell Dev Biol. 2021 Nov 01;9:739079. (PMID: 34858975)
PLoS One. 2020 Sep 14;15(9):e0238926. (PMID: 32925940)
Mol Biol Cell. 2016 Jun 15;27(12):1948-57. (PMID: 27099372)
PLoS One. 2014 Sep 11;9(9):e107088. (PMID: 25210770)
BMC Bioinformatics. 2019 Jun 28;20(1):360. (PMID: 31253078)
Biophys J. 1991 Oct;60(4):910-21. (PMID: 1742458)
Sci Rep. 2017 Jun 7;7(1):2999. (PMID: 28592874)
Ann Anat. 2014 Jan;196(1):20-5. (PMID: 23773475)
PLoS One. 2017 Jun 29;12(6):e0180400. (PMID: 28662210)
Med Image Anal. 2012 May;16(4):904-14. (PMID: 22377657)
Annu Rev Biophys. 2023 May 9;52:139-160. (PMID: 37159293)
Elife. 2022 Nov 29;11:. (PMID: 36444654)
Nat Commun. 2021 Apr 15;12(1):2276. (PMID: 33859193)
Elife. 2015 Feb 12;4:. (PMID: 25675087)
Cell. 2021 Sep 2;184(18):4819-4837.e22. (PMID: 34380046)
Sci Rep. 2021 Jan 11;11(1):323. (PMID: 33431919)
Nat Methods. 2021 Dec;18(12):1427-1440. (PMID: 34862501)
Comput Struct Biotechnol J. 2023 Mar 09;21:2018-2034. (PMID: 36968017)
PLoS One. 2021 Apr 16;16(4):e0250093. (PMID: 33861785)
PLoS Comput Biol. 2010 Jul 08;6(7):e1000853. (PMID: 20628576)
Biomaterials. 1999 Dec;20(23-24):2235-44. (PMID: 10614930)
BMC Bioinformatics. 2012;13 Suppl 16:S11. (PMID: 23176142)
J Struct Biol. 2005 Aug;151(2):182-95. (PMID: 16043363)
J Microsc. 2025 Dec;300(3):384-408. (PMID: 40879663)
Biophys J. 2003 Aug;85(2):1289-306. (PMID: 12885672)
Nat Commun. 2023 May 9;14(1):2681. (PMID: 37160944)
Mol Biol Cell. 2016 Nov 7;27(22):3616-3626. (PMID: 27535428)
Sci Rep. 2018 Sep 12;8(1):13658. (PMID: 30209281)
Ann Bot. 2014 Sep;114(4):829-40. (PMID: 24989783)
Am J Physiol Cell Physiol. 2011 Apr;300(4):C723-42. (PMID: 21209361)
J Cell Biol. 2014 Jan 20;204(2):231-45. (PMID: 24446482)
F1000Res. 2021 Apr 26;10:320. (PMID: 34136134)
Nat Rev Methods Primers. 2021;1:. (PMID: 35663461)
BMC Biol. 2022 Aug 11;20(1):178. (PMID: 35953853)
Patterns (N Y). 2020 Jun 12;1(3):100038. (PMID: 33205106)
Traffic. 2017 Jan;18(1):71-88. (PMID: 27770501)
Mol Biol Cell. 2023 May 15;34(6):ar50. (PMID: 36515991)
Nat Methods. 2021 Dec;18(12):1418-1422. (PMID: 34021280)
J Cell Biol. 2023 Feb 6;222(2):. (PMID: 36534166)
PLoS One. 2014 Jan 23;9(1):e86646. (PMID: 24466185)
Nat Methods. 2010 Jul;7(7):547-53. (PMID: 20543845)
Sci Rep. 2022 Jan 7;12(1):167. (PMID: 34997100)
Nat Commun. 2023 Apr 3;14(1):1854. (PMID: 37012230)
Wellcome Open Res. 2021 Feb 22;6:37. (PMID: 33954267)
J Microsc. 2006 Dec;224(Pt 3):213-32. (PMID: 17210054)
Plants (Basel). 2023 Feb 24;12(5):. (PMID: 36903900)
Comput Methods Programs Biomed. 2022 Dec;227:107211. (PMID: 36356384)
Prostate. 2007 Feb 15;67(3):248-54. (PMID: 17075809)
PLoS One. 2022 Nov 18;17(11):e0276972. (PMID: 36399435)
PLoS One. 2011;6(11):e27385. (PMID: 22110636)
FASEB J. 2021 May;35(5):e21582. (PMID: 33835502)
Elife. 2019 Aug 13;8:. (PMID: 31405451)
Biophys J. 2006 Feb 15;90(4):1439-52. (PMID: 16326902)
FEBS Lett. 2022 Oct;596(19):2472-2485. (PMID: 35833863)
Med Image Anal. 2019 Aug;56:44-67. (PMID: 31181343)
Am J Physiol Endocrinol Metab. 2020 Feb 1;318(2):E87-E101. (PMID: 31846372)
Front Physiol. 2022 Jan 28;13:832417. (PMID: 35153840)
Front Cell Dev Biol. 2022 Sep 30;10:898351. (PMID: 36247011)
J Microsc. 1990 Feb;157(Pt 2):149-62. (PMID: 2313683)
Biophys J. 2011 Jun 8;100(11):2820-8. (PMID: 21641328)
Plant J. 2016 Nov;88(3):468-475. (PMID: 27354251)
Cytometry A. 2011 Jul;79(7):545-59. (PMID: 21674772)
Nat Methods. 2023 Apr;20(4):569-579. (PMID: 36997816)
J Theor Biol. 2007 Feb 21;244(4):597-620. (PMID: 17074362)
J Anat. 1953 Oct;87(4):387-406. (PMID: 13117757)
IEEE Rev Biomed Eng. 2016;9:234-63. (PMID: 26742143)
Nat Methods. 2022 Jul;19(7):829-832. (PMID: 35654950)
PLoS One. 2016 Aug 09;11(8):e0160735. (PMID: 27505420)
Science. 2017 Apr 14;356(6334):186-189. (PMID: 28408602)
Grant Information:
Center for Scalable Data Analytics and Artificial Intelligence Dresden/Leipzig
Contributed Indexing:
Keywords: bioimage analysis; biological imaging; decision tree; image processing; microscopy
Entry Date(s):
Date Created: 20250829 Date Completed: 20251121 Latest Revision: 20251123
Update Code:
20251123
PubMed Central ID:
PMC12637018
DOI:
10.1111/jmi.70021
PMID:
40879663
Database:
MEDLINE
Weitere Informationen
Bioimaging has transformed our understanding of biological processes, yet extracting meaningful information from complex datasets remains a challenge, particularly for biologists without computational expertise. This paper proposes a simple general approach, to help identify which image analysis methods could be relevant for a given image dataset. We first categorise structures commonly observed in bioimage data into different types related to image analysis domains. Based on these types, we provide a list of methods adapted to the quantification of images from each category. Our approach includes illustrative examples and a visual flowchart, to help researchers define analysis objectives clearly. By understanding the diversity of bioimage structures and linking them with appropriate analysis approaches, the framework empowers researchers to navigate bioimage datasets more efficiently. It also aims to foster a common language between researchers and analysts, thereby enhancing mutual understanding and facilitating effective communication.
(© 2025 The Author(s). Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.)