1. Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Wei O, Li B, Yang B, Tsuchida MA, Chhun BB, Zhang G, Mei R, Anderson M, Shepherd D, Hunt-Isaak I, Dunn RL, Jahr W, Kato S, Royer LA, Thiagarajah J, Eliceiri K, Lundberg E, Mehta SB, Waller L. Pycro-Manager: open-source software for customized and reproducible microscope control. Nat Methods. 2020 Jun 19;18:226–228. PMCID: PMC8532176
2. Schroeder AB, Dobson ETA, Rueden CT, Tomancak P, Jug F, Eliceiri KW. The ImageJ ecosystem: Open-source software for image visualization, processing, and analysis. Protein Sci. Wiley Online Library; 2021;30(1):234–249. PMCID: PMC7737784
3. Li B, Li Y, Eliceiri KW. Dual-stream multiple instance learning network for whole slide image classification with self-supervised contrastive learning. 2021 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). IEEE; 2021. PMCID: PMC8765709
4. Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics. BioMed Central; 2021 Sep 10;22(1):433. PMCID: PMC8431850
5. Stirling DR, Carpenter AE, Cimini BA. CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis. Bioinformatics. Oxford University Press; 2021 Nov 5;37(21):3992–3994. PMCID: PMC10186093
6. Reinke A, Tizabi MD, Sudre CH, Eisenmann M, Rädsch T, Baumgartner M, Acion L, Antonelli M, Arbel T, Bakas S, Bankhead P, Benis A, Blaschko M, Buettner F, Jorge Cardoso M, Chen J, Cheplygina V, Christodoulou E, Cimini B, Collins GS, Engelhardt S, Farahani K, Ferrer L, Galdran A, van Ginneken B, Glocker B, Godau P, Haase R, Hamprecht F, Hashimoto DA, Heckmann-Nötzel D, Hirsch P, Hoffman MM, Huisman M, Isensee F, Jannin P, Kahn CE, Kainmueller D, Kainz B, Karargyris A, Karthikesalingam A, Emre Kavur A, Kenngott H, Kleesiek J, Kleppe A, Kohler S, Kofler F, Kopp-Schneider A, Kooi T, Kozubek M, Kreshuk A, Kurc T, Landman BA, Litjens G, Madani A, Maier-Hein K, Martel AL, Mattson P, Meijering E, Menze B, Moher D, Moons KGM, Müller H, Nichyporuk B, Nickel F, Alican Noyan M, Petersen J, Polat G, Rafelski SM, Rajpoot N, Reyes M, Rieke N, Riegler M, Rivaz H, Saez-Rodriguez J, Sánchez CI, Schroeter J, Saha A, Alper Selver M, Sharan L, Shetty S, van Smeden M, Stieltjes B, Summers RM, Taha AA, Tiulpin A, Tsaftaris SA, Van Calster B, Varoquaux G, Wiesenfarth M, Yaniv ZR, Jäger P, Maier-Hein L. Common limitations of image processing metrics: A picture story. arXiv preprint arXiv:2104. 05642. 2021.
7. Lucas AM, Ryder PV, Li B, Cimini BA, Eliceiri KW, Carpenter AE. Open-source deep-learning software for bioimage segmentation. Mol Biol Cell. Am Soc Cell Biol; 2021 Apr 19;32(9):823–829. PMCID: PMC8108523
8. Liu JTC, Glaser AK, Bera K, True LD, Reder NP, Eliceiri KW, Madabhushi A. Harnessing non-destructive 3D pathology. Nat Biomed Eng. 2021 Mar;5(3):203–218. PMCID: PMC8118147
9. Levet F, Carpenter AE, Eliceiri K, Kreshuk A, Bankhead P, Haase R. Developing open-source software for bioimage analysis: opportunities and challenges. F1000Res. 2021 Apr 19;10. PMCID: PMC8226416
10. Gahm NA, Rueden CT, Evans EL 3rd, Selzer G, Hiner MC, Chacko JV, Gao D, Sherer NM, Eliceiri KW. New Extensibility and Scripting Tools in the ImageJ Ecosystem. Curr Protoc. 2021 Aug;1(8):e204. PMCID: PMC8363112
11. Dobson ETA, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW. ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Curr Protoc. Wiley Online Library; 2021 May;1(5):e89. PMCID: PMC8450896
12. Mukherjee L, Sagar MAK, Ouellette JN, Watters JJ, Eliceiri KW. A deep learning framework for classifying microglia activation state using morphology and intrinsic fluorescence lifetime data. Front Neuroinform. 2022 Dec 16;16:1040008. PMCID: PMC9803172
13. Rueden CT, Hiner MC, Evans EL 3rd, Pinkert MA, Lucas AM, Carpenter AE, Cimini BA, Eliceiri KW. PyImageJ: A library for integrating ImageJ and Python. Nat Methods. Nature Publishing Group; 2022 Nov;19(11):1326–1327. PMCID: PMC9783691
14. Jamali N, Dobson ET, Eliceiri KW, Carpenter AE, Cimini BA. 2020 BioImage Analysis Survey: Community experiences and needs for the future. Biol Imaging. Cambridge University Press; 2022;1:e4. PMCID: PMC8982832
15. Keller D, Stinus S, Umlauf D, Gourbeyre E, Biot E, Olivier N, Mahou P, Beaurepaire E, Andrey P, Crabbe L. Spatial modeling of telomere intra-nuclear distribution reveals non-random organization that varies during cell cycle and depends on LAP2 and BAF. bioRxiv. 2022 Dec 22;
16. Cimini BA. Improved tracking via cell region fingerprints. Nat Methods. Nature Publishing Group; 2022 Oct;19(10):1177–1178. PMCID: PMC10275404
17. Li B, Nelson MS, Savari O, Loeffler AG, Eliceiri KW. Differentiation of pancreatic ductal adenocarcinoma and chronic pancreatitis using graph neural networks on histopathology and collagen fiber features. J Pathol Inform. 2022 Nov 19;13:100158. PMCID: PMC9808020
18. Schlaeppi A, Adams W, Haase R, Huisken J, MacDonald RB, Eliceiri KW, Kugler EC. Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration. Frontiers in Bioinformatics. Frontiers; 2022 Apr;2:40. PMCID: PMC9122012
19. Evans EL 3rd, Pocock GM, Einsdorf G, Behrens RT, Dobson ETA, Wiedenmann M, Birkhold C, Ahlquist P, Eliceiri KW, Sherer NM. HIV RGB: Automated Single-Cell Analysis of HIV-1 Rev-Dependent RNA Nuclear Export and Translation Using Image Processing in KNIME. Viruses. 2022 Apr 26;14(5). PMCID: PMC9145009
20. Ma J, Xie R, Ayyadhury S, Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, Wang Y, Han L, Yang X, Labagnara M, Gligorovski V, Scheder M, Rahi SJ, Kempster C, Pollitt A, Espinosa L, Mignot T, Middeke JM, Eckardt JN, Li W, Li Z, Cai X, Bai B, Greenwald NF, Van Valen D, Weisbart E, Cimini BA, Cheung T, Brück O, Bader GD, Wang B. The multi-modality cell segmentation challenge: Towards universal solutions. Nat Methods. 2023 Aug 10; PMCID: 10019067
21. Ouyang W, Eliceiri KW, Cimini BA. Moving beyond the desktop: prospects for practical bioimage analysis via the web. Front Bioinform. 2023 Jul 25;3:1233748. PMCID: PMC10409478
22. McCarty SM, Clasby MC, Sexton JZ. Automated high-throughput, high-content 3D imaging of intact pancreatic islets. SLAS Discov. 2023 Jul 31;28(7):316–324. PMID: 37527729
23. Zhang P, Rumschitzki D, Edwards RH. High-speed imaging reveals the bimodal nature of dense core vesicle exocytosis. Proc Natl Acad Sci USA. 2023 Jan 3;120(1):e2214897120. PMCID: PMC9910497
24. Park H, Li B, Liu Y, Nelson MS, Wilson HM, Sifakis E, Eliceiri KW. Collagen fiber centerline tracking in fibrotic tissue via deep neural networks with variational autoencoder-based synthetic training data generation. Med Image Anal. Elsevier; 2023;90:102961. PMCID: PMC10591913
25. Volpe G, Wählby C, Tian L, Hecht M, Yakimovich A, Monakhova K, Waller L, Sbalzarini IF, Metzler CA, Xie M, Zhang K, Lenton ICD, Rubinsztein-Dunlop H, Brunner D, Bai B, Ozcan A, Midtvedt D, Wang H, Sladoje N, Lindblad J, Smith JT, Ochoa M, Barroso M, Intes X, Qiu T, Yu LY, You S, Liu Y, Ziatdinov MA, Kalinin SV, Sheridan A, Manor U, Nehme E, Goldenberg O, Shechtman Y, Moberg HK, Langhammer C, Špačková B, Helgadottir S, Midtvedt B, Argun A, Thalheim T, Cichos F, Bo S, Hubatsch L, Pineda J, Manzo C, Bachimanchi H, Selander E, Homs-Corbera A, Fränzl M, de Haan K, Rivenson Y, Korczak Z, Adiels CB, Mijalkov M, Veréb D, Chang YW, Pereira JB, Matuszewski D, Kylberg G, Sintorn IM, Caicedo JC, Cimini BA, Bell MAL, Saraiva BM, Jacquemet G, Henriques R, Ouyang W, Le T, Gómez-de-Mariscal E, Sage D, Muñoz-Barrutia A, Lindqvist EJ, Bergman J. Roadmap on Deep Learning for Microscopy. ArXiv. 2023. PMCID: PMC10029045
26. Romero S, Unchwaniwala N, Evans EL 3rd, Eliceiri KW, Loeb DD, Sherer NM. Live Cell Imaging Reveals HBV Capsid Translocation from the Nucleus To the Cytoplasm Enabled by Cell Division. MBio. 2023 Apr 25;14(2):e0330322. PMCID: PMC10127671
27. Senft RA, Diaz-Rohrer B, Colarusso P, Swift L, Jamali N, Jambor H, Pengo T, Brideau C, Llopis PM, Uhlmann V, Kirk J, Gonzales KA, Bankhead P, Evans EL 3rd, Eliceiri KW, Cimini BA. A biologist’s guide to planning and performing quantitative bioimaging experiments. PLoS Biol. Public Library of Science; 2023 Jun 1;21(6):e3002167. PMCID: PMC10298797
28. Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Casas Moreno X, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Küpcü Yoldaş A, Kyoda K, le Tournoulx de la Villegeorges A, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR. OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochem Cell Biol. Springer Berlin Heidelberg Berlin/Heidelberg; 2023 Jul 10;160(3):223–251. PMCID: 3437820
29. Weisbart E, Tromans-Coia C, Diaz-Rohrer B, Stirling DR, Garcia-Fossa F, Senft RA, Hiner MC, de Jesus MB, Eliceiri KW, Cimini BA. CellProfiler plugins - An easy image analysis platform integration for containers and Python tools. J Microsc. 2023 Sep 10; PMCID: PMC10924770
30. Li B, Nelson MS, Chacko JV, Cudworth N, Eliceiri KW. Hardware-software co-design of an open-source automatic multimodal whole slide histopathology imaging system. J Biomed Opt. 2023 Feb;28(2):026501. PMCID: PMC9905038
31. Carpenter AE, Cimini BA, Eliceiri KW. Smart microscopes of the future. Nat Methods. Nature Publishing Group; 2023 Jul;20(7):962–964. PMCID: PMC10448787
32. Selzer GJ, Rueden CT, Hiner MC, Evans EL 3rd, Harrington KIS, Eliceiri KW. Napari-imageJ: ImageJ ecosystem access from napari. Nat Methods. 2023 Oct;20(10):1443–1444. PMCID: PMC10591722
33. 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. J Microsc. 2023 Jun 5; PMCID: PMC10950841
34. Garcia-Fossa F, Cruz MC, Haghighi M, de Jesus MB, Singh S, Carpenter AE, Cimini BA. Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization. Current Protocols. Wiley Online Library; 2023 Mar;3(3):e713. PMCID: PMC10027367
35. Weisbart E, Cimini BA. Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale. Nat Methods. Nature Publishing Group US New York; 2023 Aug;20(8):1120–1121. PMCID: 6029841
36. Li Z, Li B, Eliceiri KW, Narayanan V. Computationally efficient adaptive decompression for whole slide image processing. Biomed Opt Express. Optica Publishing Group; 2023;14(2):667–686. PMCID: PMC9979681
37. Cimini BA, Eliceiri KW. The Twenty Questions of Bioimage Object Analysis. Nat Methods. Nature Publishing Group; 2023 Jul;20(7):976–978. PMCID: PMC10561713
38. Stanton AC, Lagerborg KA, Tellez L, Krunnfusz A, King EM, Ye S, Solomon IH, Tabebordbar M, Sabeti PC. Systemic administration of novel engineered AAV capsids facilitates enhanced transgene expression in the macaque CNS. Med. 2023 Jan 13;4(1):31–50.e8. PMCID: PMC9840684
39. Tan KKD, Tsuchida MA, Chacko JV, Gahm NA, Eliceiri KW. Real-time open-source FLIM analysis. Front Bioinform. 2023 Nov 30;3:1286983. PMCID: PMC10720713
40. 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. Nature Publishing Group US New York; 2024 Feb;21(2):170–181. PMCID: PMC10922596
41. Cimini BA. Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. J Microsc. 2024 Mar 27; PMID: 38532662
42. Haase R, Tischer C, Bankhead P, Miura K, Cimini B. A Call for FAIR and Open-Access Training Materials to advance Bioimage Analysis. OSF preprints. 2024.
43. Bajcsy P, Bhattiprolu S, Borner K, Cimini B, Collinson L, Ellenberg J, Fiolka R, Giger M, Goscinski W, Hartley M, Hotaling N, Horwitz R, Jug F, Kreshuk A, Lundberg E, Mathur A, Narayan K, Onami S, Plant AL, Prior F, Swedlow J, Taylor A, Keppler A. Enabling global Image Data sharing in the life sciences. arXiv preprint arXiv:2401. 13023. 2024.
44. Cimini B, Bankhead P, D’Antuono R, Elnaz F, Fernandez-Rodriguez J, Fuster-Barceló C, Haase R, Jambor H, Jones ML, Jug F, Klemm A, Kreshuk A, Marcotti S, Martins GG, McArdle S, Muñoz Barrutia A, Murphy L, Nelson M, Nørrelykke S, Paul-Gilloteaux P, Pengo T, Pylvänäinen J, Pytowski L, Ravera A, Reinke A, Rekik Y, Strambio-De-Castillia C, Thédié D, Uhlmann V, Umney O, Wiggins L, Eliceiri K. The Crucial Role of BioImage Analysts in Scientific Research and Publication. Zenodo. 2024.
45. Moser LM, Gogoberidze N, Papaleo A, Lucas A, Dao D, Friedrich CA, Paavolainen L, Molnar C, Stirling DR, Hung J, Wang R, Tromans-Coia C, Li B, Evans EL, Eliceiri KW, Horvath P, Carpenter AE, Cimini BA. Piximi - An Images to Discovery web tool for bioimages and beyond. bioRxiv. 2024 [cited 2024 Jun 5]. p. 2024.06.03.597232.
46. Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini B, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg J, Spraggins JM, Sudar D, Vierdag WMAM, Volkmann N, Wählby C, Siyuan, Wang, Yaniv Z, Strambio-De-Castillia C. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. arXiv [q-bio.OT]. 2024. PMCID: PMC10862930
47. Weisbart E, Kumar A, Arevalo J, Carpenter AE, Cimini BA, Singh S. Cell Painting Gallery: an open resource for image-based profiling. arXiv [q-bio.QM]. 2024. PMCID: PMC10862924
48. Selzer GJ, Rueden CT, Hiner MC, Evans EL III, Kolb D, Wiedenmann M, Birkhold C, Buchholz TO, Helfrich S, Northan B, Walter A, Schindelin J, Pietzsch T, Saalfeld S, Berthold MR, Eliceiri KW. SciJava Ops: An improved algorithms framework for Fiji and beyond. arXiv preprint arXiv:2405. 12385. 2024.
49. De Niz M, Escobedo García R, Terán Ramirez C, Pakowski Y, Abonza Y, Bialy N, Orr VL, Olivera A, Abonza V, Alleva K, Allodi S, Almeida MF, Becerril Cuevas AR, Bonnet F, Burgos Solorio A, Chew TL, Chiabrando G, Cimini B, Cleret-Buhot A, Contreras Jiménez G, Daza L, De Sá V, De Val N, Delgado-Álvarez DL, Eliceiri K, Fiolka R, Grecco H, Hanein D, Hernández Herrera P, Hockberger P, Hernandez HO, Hernandez Guadarrama Y, Itano M, Jacobs CA, Jiménez-García LF, Jiménez Sabinina V, Kamaid A, Keppler A, Kumar A, Lacoste J, Lovy A, Luby-Phelps K, Mahadevan-Jansen A, Malacrida L, Mehta SB, Miller C, Miranda K, Moore JA, North A, O’Toole P, Olivares Urbano M, Pietrasanta LI, Portugal RV, Rossi AH, Sanchez Contreras J, Strambio-De-Castilla C, Soldevila G, Vale B, Vazquez D, Wood C, Brown CM, Guerrero A. Building momentum through networks: Bioimaging across the Americas. J Microsc. John Wiley & Sons, Ltd; 2024 May 15;294(n/a):420–439. PMID: 38747464
50. Cimini BA, Tromans-Coia C, Stirling DR, Sivagurunathan S, Senft RA, Ryder PV, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz MC, Weisbart E, Carpenter AE. A Postdoctoral Training Program in Bioimage Analysis. bioRxiv. 2024 [cited 2024 May 16]. p. 2024.05.13.593910. PMCID: PMC11118354
51. Boucau J, Naidoo T, Liu Y, Dasgupta S, Jain N, Castillo JR, Jacobson NE, Nargan K, Cimini BA, Eliceiri KW, Steyn AJC, Barczak AK. A mouse model of TB-associated lung fibrosis reveals persistent inflammatory macrophage populations during treatment. bioRxiv. 2024 [cited 2024 Jun 7]. p. 2024.06.04.597479.
52. Riendeau JM, Gillette A, Guzman EC, Cruz MC, Kralovec A, Udgata S, Schmitz A, Deming DA, Cimini BA, Skala MC. Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images. bioRxiv. 2024 [cited 2024 Jun 10]. p. 2024.06.07.597994.