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For: Aaron J, Chew TL. A guide to accurate reporting in digital image processing - can anyone reproduce your quantitative analysis? J Cell Sci 2021;134:134/6/jcs254151. [PMID: 33785609 DOI: 10.1242/jcs.254151] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
Number Cited by Other Article(s)
1
Pylvänäinen JW, Grobe H, Jacquemet G. Practical considerations for data exploration in quantitative cell biology. J Cell Sci 2025;138:jcs263801. [PMID: 40190255 PMCID: PMC12045597 DOI: 10.1242/jcs.263801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2025]  Open
2
Wang J, Zhang Y, Chen H, Wu Y, Liu J, Che H, Zhang Y, Zhu X. Motor-Cargo Structured Nanotractors for Augmented NIR Phototherapy via Gas-Boosted Tumor Penetration and Respiration-Impaired Mitochondrial Dysfunction. Adv Healthc Mater 2024:e2402063. [PMID: 39380347 DOI: 10.1002/adhm.202402063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 09/26/2024] [Indexed: 10/10/2024]
3
Imreh G, Hu J, Le Guyader S. Improving light microscopy training routines with evidence-based education. J Microsc 2024;294:295-307. [PMID: 37534621 DOI: 10.1111/jmi.13216] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023]
4
Sytwu K, Rangel DaCosta L, Scott MC. Generalization Across Experimental Parameters in Neural Network Analysis of High-Resolution Transmission Electron Microscopy Datasets. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2024;30:85-95. [PMID: 38285915 DOI: 10.1093/micmic/ozae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/19/2023] [Accepted: 01/06/2024] [Indexed: 01/31/2024]
5
Jan M, Spangaro A, Lenartowicz M, Mattiazzi Usaj M. From pixels to insights: Machine learning and deep learning for bioimage analysis. Bioessays 2024;46:e2300114. [PMID: 38058114 DOI: 10.1002/bies.202300114] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 12/08/2023]
6
Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho MT, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Le Dévédec S, Le Guyader S, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK. Community-developed checklists for publishing images and image analyses. Nat Methods 2024;21:170-181. [PMID: 37710020 PMCID: PMC10922596 DOI: 10.1038/s41592-023-01987-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/26/2023] [Indexed: 09/16/2023]
7
Lee RM, Eisenman LR, Khuon S, Aaron JS, Chew TL. Believing is seeing - the deceptive influence of bias in quantitative microscopy. J Cell Sci 2024;137:jcs261567. [PMID: 38197776 DOI: 10.1242/jcs.261567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]  Open
8
Jambor HK. A community-driven approach to enhancing the quality and interpretability of microscopy images. J Cell Sci 2023;136:jcs261837. [PMID: 38095680 DOI: 10.1242/jcs.261837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]  Open
9
Bianchini RM, Kurz EU. The analysis of protein recruitment to laser microirradiation-induced DNA damage in live cells: Best practices for data analysis. DNA Repair (Amst) 2023;129:103545. [PMID: 37524003 DOI: 10.1016/j.dnarep.2023.103545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
10
Silkotch C, Garcia-Milian R, Hersey D. Partnering with health sciences libraries to address challenges in bioimaging data management and sharing. Histochem Cell Biol 2023;160:193-198. [PMID: 37247072 DOI: 10.1007/s00418-023-02198-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 05/30/2023]
11
Helmbrecht H, Lin TJ, Janakiraman S, Decker K, Nance E. Prevalence and practices of immunofluorescent cell image processing: a systematic review. Front Cell Neurosci 2023;17:1188858. [PMID: 37545881 PMCID: PMC10400723 DOI: 10.3389/fncel.2023.1188858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023]  Open
12
Sivagurunathan S, Marcotti S, Nelson CJ, Jones ML, Barry DJ, Slater TJA, Eliceiri KW, Cimini BA. Bridging Imaging Users to Imaging Analysis - A community survey. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543701. [PMID: 37333353 PMCID: PMC10274673 DOI: 10.1101/2023.06.05.543701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
13
Gorman C, Punzo D, Octaviano I, Pieper S, Longabaugh WJR, Clunie DA, Kikinis R, Fedorov AY, Herrmann MD. Interoperable slide microscopy viewer and annotation tool for imaging data science and computational pathology. Nat Commun 2023;14:1572. [PMID: 36949078 PMCID: PMC10033920 DOI: 10.1038/s41467-023-37224-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023]  Open
14
Larsen DD, Gaudreault N, Gibbs HC. Reporting reproducible imaging protocols. STAR Protoc 2023;4:102040. [PMID: 36861824 PMCID: PMC9996438 DOI: 10.1016/j.xpro.2022.102040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/21/2022] [Accepted: 12/29/2022] [Indexed: 03/03/2023]  Open
15
Wallmeier K, Würthwein T, Lemberger N, Brinkmann M, Hellwig T, Fallnich C. Frequency modulation stimulated Raman scattering scheme for real-time background correction with a single light source. BIOMEDICAL OPTICS EXPRESS 2023;14:315-325. [PMID: 36698676 PMCID: PMC9841997 DOI: 10.1364/boe.476513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
16
Practical considerations for quantitative light sheet fluorescence microscopy. Nat Methods 2022;19:1538-1549. [PMID: 36266466 DOI: 10.1038/s41592-022-01632-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/31/2022] [Indexed: 12/25/2022]
17
Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy. Nat Biotechnol 2022;40:606-617. [PMID: 34782739 DOI: 10.1038/s41587-021-01092-2] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/10/2021] [Indexed: 02/07/2023]
18
Reiche MA, Aaron JS, Boehm U, DeSantis MC, Hobson CM, Khuon S, Lee RM, Chew TL. When light meets biology - how the specimen affects quantitative microscopy. J Cell Sci 2022;135:274812. [PMID: 35319069 DOI: 10.1242/jcs.259656] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]  Open
19
Lu V, Roy IJ, Torres A, Joly JH, Ahsan FM, Graham NA, Teitell MA. Glutamine-dependent signaling controls pluripotent stem cell fate. Dev Cell 2022;57:610-623.e8. [PMID: 35216682 PMCID: PMC8930616 DOI: 10.1016/j.devcel.2022.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/01/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022]
20
Martinez AL, Shannon MJ, Eisman SE, Hegewisch-Solloa E, Asif AN, Ebrahim TAM, Mace EM. Quantifying Human Natural Killer Cell Migration by Imaging and Image Analysis. Methods Mol Biol 2022;2463:129-151. [PMID: 35344172 PMCID: PMC9159076 DOI: 10.1007/978-1-0716-2160-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
21
Sanchez-Arias JC, Carrier M, Frederiksen SD, Shevtsova O, McKee C, van der Slagt E, Gonçalves de Andrade E, Nguyen HL, Young PA, Tremblay MÈ, Swayne LA. A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy. Front Neuroanat 2021;15:722443. [PMID: 34949993 PMCID: PMC8691181 DOI: 10.3389/fnana.2021.722443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023]  Open
22
Ryan J, Pengo T, Rigano A, Llopis PM, Itano MS, Cameron LA, Marqués G, Strambio-De-Castillia C, Sanders MA, Brown CM. MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text. Nat Methods 2021;18:1414-1416. [PMID: 34654919 PMCID: PMC9488561 DOI: 10.1038/s41592-021-01290-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
23
Montero Llopis P, Senft RA, Ross-Elliott TJ, Stephansky R, Keeley DP, Koshar P, Marqués G, Gao YS, Carlson BR, Pengo T, Sanders MA, Cameron LA, Itano MS. Best practices and tools for reporting reproducible fluorescence microscopy methods. Nat Methods 2021;18:1463-1476. [PMID: 34099930 DOI: 10.1038/s41592-021-01156-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 02/04/2023]
24
Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM, Corbett AD, Faklaris O, Lacoste J, Laude A, Nelson G, Nitschke R, Farzam F, Smith CS, Grunwald D, Strambio-De-Castillia C. Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Nat Methods 2021;18:1427-1440. [PMID: 34862501 PMCID: PMC9271325 DOI: 10.1038/s41592-021-01327-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
25
Laine RF, Arganda-Carreras I, Henriques R, Jacquemet G. Avoiding a replication crisis in deep-learning-based bioimage analysis. Nat Methods 2021;18:1136-1144. [PMID: 34608322 PMCID: PMC7611896 DOI: 10.1038/s41592-021-01284-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
26
Hmeljak J, Agullo-Pascual E. Celebrating FocalPlane and microscopy in Disease Models & Mechanisms. Dis Model Mech 2021;14:270975. [PMID: 34279567 DOI: 10.1242/dmm.049183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
27
Heddleston JM, Aaron JS, Khuon S, Chew TL. A guide to accurate reporting in digital image acquisition - can anyone replicate your microscopy data? J Cell Sci 2021;134:134/6/jcs254144. [PMID: 33785608 DOI: 10.1242/jcs.254144] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
28
Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C. Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. Nat Methods 2021;18:1489-1495. [PMID: 34862503 PMCID: PMC8648560 DOI: 10.1038/s41592-021-01315-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/30/2021] [Indexed: 12/31/2022]
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