{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T03:29:41Z","timestamp":1767324581078,"version":"3.48.0"},"publisher-location":"Cham","reference-count":38,"publisher":"Springer Nature Switzerland","isbn-type":[{"value":"9783032128393","type":"print"},{"value":"9783032128409","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026]]},"DOI":"10.1007\/978-3-032-12840-9_24","type":"book-chapter","created":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T03:26:13Z","timestamp":1767324373000},"page":"369-383","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["SubCellSAM: Zero-Shot (Sub-)Cellular Segmentation for\u00a0Hit Validation in\u00a0Drug Discovery"],"prefix":"10.1007","author":[{"given":"Jacob","family":"Hanimann","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Siegismund","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario","family":"Wieser","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephan","family":"Steigele","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,1,2]]},"reference":[{"key":"24_CR1","unstructured":"Alayrac, et al.: Flamingo: a visual language model for few-shot learning. In: Advances in Neural Information Processing Systems (2022)"},{"key":"24_CR2","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1038\/s41592-024-02580-4","volume":"22","author":"A Archit","year":"2025","unstructured":"Archit, A., et al.: Segment anything for microscopy. Nat. Methods 22, 579\u2013591 (2025). https:\/\/doi.org\/10.1038\/s41592-024-02580-4","journal-title":"Nat. Methods"},{"key":"24_CR3","doi-asserted-by":"publisher","unstructured":"Barcelos, M.P., et al.: Lead optimization in drug discovery. In: Taft, C.A., de Lazaro, S.R. (eds) Research Topics in Bioactivity, Environment and Energy. Engineering Materials, pp. 481\u2013500. Springer, Cham (2022). https:\/\/doi.org\/10.1007\/978-3-031-07622-0_19","DOI":"10.1007\/978-3-031-07622-0_19"},{"issue":"9","key":"24_CR4","doi-asserted-by":"publisher","first-page":"1757","DOI":"10.1038\/nprot.2016.105","volume":"11","author":"MA Bray","year":"2016","unstructured":"Bray, M.A., et al.: Cell painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat. Protoc. 11(9), 1757\u20131774 (2016). https:\/\/doi.org\/10.1038\/nprot.2016.105","journal-title":"Nat. Protoc."},{"key":"24_CR5","unstructured":"Brown, T., et al.: Language models are few-shot learners. In: Advances in Neural Information Processing Systems (2020)"},{"key":"24_CR6","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1038\/nmeth.4397","volume":"14","author":"JC Caicedo","year":"2017","unstructured":"Caicedo, J.C., et al.: Data-analysis strategies for image-based cell profiling. Nat. Methods 14, 849\u2013863 (2017). https:\/\/doi.org\/10.1038\/nmeth.4397","journal-title":"Nat. Methods"},{"key":"24_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2006-7-10-r100","volume":"7","author":"AE Carpenter","year":"2006","unstructured":"Carpenter, A.E., et al.: Cellprofiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, 1\u201311 (2006). https:\/\/doi.org\/10.1186\/gb-2006-7-10-r100","journal-title":"Genome Biol."},{"issue":"13","key":"24_CR8","doi-asserted-by":"publisher","first-page":"2010","DOI":"10.1093\/bioinformatics\/btx069","volume":"33","author":"WJ Godinez","year":"2017","unstructured":"Godinez, W.J., Hossain, I., Lazic, S.E., Davies, J.W., Zhang, X.: A multi-scale convolutional neural network for phenotyping high-content cellular images. Bioinformatics 33(13), 2010\u20132019 (2017). https:\/\/doi.org\/10.1093\/bioinformatics\/btx069","journal-title":"Bioinformatics"},{"key":"24_CR9","doi-asserted-by":"crossref","unstructured":"Guo, M., Yi, H., Qin, Z., Wang, H., Men, A., Lao, Q.: Multiple prompt fusion for zero-shot lesion detection using vision-language models. In: 26th International Conference on Medical Image Computing and Computer Assisted Intervention (2023)","DOI":"10.1007\/978-3-031-43904-9_28"},{"key":"24_CR10","doi-asserted-by":"crossref","unstructured":"Gupta, A., Vuillecard, P., Farkhondeh, A., Odobez, J.M.: Exploring the zero-shot capabilities of vision-language models for improving gaze following. In: IEEE\/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops (2024)","DOI":"10.1109\/CVPRW63382.2024.00066"},{"key":"24_CR11","doi-asserted-by":"crossref","unstructured":"Han, G., Lim, S.N.: Few-shot object detection with foundation models. In: IEEE\/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (2024)","DOI":"10.1109\/CVPR52733.2024.02703"},{"key":"24_CR12","doi-asserted-by":"crossref","unstructured":"Israel, U., et al.: A foundation model for cell segmentation (2023). https:\/\/arxiv.org\/abs\/2311.11004","DOI":"10.1101\/2023.11.17.567630"},{"key":"24_CR13","doi-asserted-by":"crossref","unstructured":"Karras, T., Laine, S., Aittala, M., Hellsten, J., Lehtinen, J., Aila, T.: Analyzing and improving the image quality of styleGAN. In: IEEE\/CVF Conference on Computer Vision and Pattern Recognition (CVPR) (2020)","DOI":"10.1109\/CVPR42600.2020.00813"},{"key":"24_CR14","unstructured":"Ke, L., et al.: Segment anything in high quality. In: Advances in Neural Information Processing Systems (2023)"},{"key":"24_CR15","doi-asserted-by":"crossref","unstructured":"Kirillov, A., et al.: Segment anything. In: IEEE\/CVF International Conference on Computer Vision (ICCV) (2023)","DOI":"10.1109\/ICCV51070.2023.00371"},{"key":"24_CR16","doi-asserted-by":"publisher","unstructured":"Kruger, S., et al.: Advances in cancer immunotherapy 2019 - latest trends. J. Exp. Clin. Cancer Res. 38 (2019). https:\/\/doi.org\/10.1186\/s13046-019-1266-0","DOI":"10.1186\/s13046-019-1266-0"},{"issue":"7","key":"24_CR17","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/nmeth.2083","volume":"9","author":"V Ljosa","year":"2012","unstructured":"Ljosa, V., Sokolnicki, K.L., Carpenter, A.E.: Annotated high-throughput microscopy image sets for validation. Nat. Methods 9(7), 637\u2013637 (2012). https:\/\/doi.org\/10.1038\/nmeth.2083","journal-title":"Nat. Methods"},{"issue":"7","key":"24_CR18","doi-asserted-by":"publisher","first-page":"840","DOI":"10.1177\/1087057110370895","volume":"15","author":"DJ Logan","year":"2010","unstructured":"Logan, D.J., Carpenter, A.E.: Screening cellular feature measurements for image-based assay development. J. Biomol. Screen. 15(7), 840\u2013846 (2010). https:\/\/doi.org\/10.1177\/1087057110370895","journal-title":"J. Biomol. Screen."},{"key":"24_CR19","unstructured":"Na, S., Guo, Y., Jiang, F., Ma, H., Huang, J.: Segment any cell: a SAM-based auto-prompting fine-tuning framework for nuclei segmentation (2024). https:\/\/arxiv.org\/abs\/2401.13220"},{"key":"24_CR20","doi-asserted-by":"publisher","unstructured":"Nichols, A.: High Content Screening as a Screening Tool in Drug Discovery, pp. 379\u2013387. Humana Press, Totowa (2006). https:\/\/doi.org\/10.1385\/1-59745-217-3:379","DOI":"10.1385\/1-59745-217-3:379"},{"key":"24_CR21","unstructured":"Radford, A., et al.: Learning transferable visual models from natural language supervision. In: International Conference on Machine Learning (2021)"},{"key":"24_CR22","unstructured":"Ravi, N., et al.: SAM 2: Segment anything in images and videos. In: International Conference on Learning Representations (2025)"},{"issue":"6","key":"24_CR23","doi-asserted-by":"publisher","first-page":"e2415445","DOI":"10.1001\/jamanetworkopen.2024.15445","volume":"7","author":"A Sertkaya","year":"2024","unstructured":"Sertkaya, A., Beleche, T., Jessup, A., Sommers, B.D.: Costs of drug development and research and development intensity in the us, 2000\u20132018. JAMA Netw. Open 7(6), e2415445\u2013e2415445 (2024). https:\/\/doi.org\/10.1001\/jamanetworkopen.2024.15445","journal-title":"JAMA Netw. Open"},{"key":"24_CR24","unstructured":"Siegismund, D., Wieser, M., Heyse, S., Steigele, S.: Self-supervised representation learning for high-content screening. In: International Conference on Medical Imaging with Deep Learning (2022)"},{"key":"24_CR25","doi-asserted-by":"crossref","unstructured":"Siegismund, D., Wieser, M., Heyse, S., Steigele, S.: Learning channel importance for high content imaging with interpretable deep input channel mixing. In: German Conference on Pattern Recognition (2023)","DOI":"10.1007\/978-3-031-54605-1_22"},{"issue":"7","key":"24_CR26","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1177\/2472555220918837","volume":"25","author":"S Steigele","year":"2020","unstructured":"Steigele, S., et al.: Deep learning-based HCS image analysis for the enterprise. SLAS Discov. 25(7), 812\u2013821 (2020). https:\/\/doi.org\/10.1177\/2472555220918837","journal-title":"SLAS Discov."},{"issue":"1","key":"24_CR27","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1186\/s12859-021-04344-9","volume":"22","author":"DR Stirling","year":"2021","unstructured":"Stirling, D.R., Swain-Bowden, M.J., Lucas, A.M., Carpenter, A.E., Cimini, B.A., Goodman, A.: CellProfiler 4: improvements in speed, utility and usability. BMC Bioinform. 22(1), 433 (2021). https:\/\/doi.org\/10.1186\/s12859-021-04344-9","journal-title":"BMC Bioinform."},{"key":"24_CR28","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1038\/s41592-025-02595-5","volume":"22","author":"C Stringer","year":"2025","unstructured":"Stringer, C., Pachitariu, M.: Cellpose3: one-click image restoration for improved cellular segmentation. Nat. Methods 22, 295\u2013599 (2025). https:\/\/doi.org\/10.1038\/s41592-025-02595-5","journal-title":"Nat. Methods"},{"key":"24_CR29","unstructured":"Tancik, M., et al.: Fourier features let networks learn high frequency functions in low dimensional domains. In: Advances in Neural Information Processing Systems (2020)"},{"issue":"4","key":"24_CR30","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1016\/j.synbio.2024.05.005","volume":"9","author":"J Tang","year":"2024","unstructured":"Tang, J., Du, W., Shu, Z., Cao, Z.: A generative benchmark for evaluating the performance of fluorescent cell image segmentation. Synthetic Syst. Biotechnol. 9(4), 627\u2013637 (2024). https:\/\/doi.org\/10.1016\/j.synbio.2024.05.005","journal-title":"Synthetic Syst. Biotechnol."},{"key":"24_CR31","doi-asserted-by":"crossref","unstructured":"Tewel, Y., Shalev, Y., Schwartz, I., Wolf, L.: Zero-shot image-to-text generation for visual-semantic arithmetic. In: IEEE\/CVF Conference on Computer Vision and Pattern Recognition (2022)","DOI":"10.1109\/CVPR52688.2022.01739"},{"key":"24_CR32","doi-asserted-by":"publisher","unstructured":"Uhl\u00e9n, M., et al.: Tissue-based map of the human proteome. Science 347(6220), 1260419 (2015). https:\/\/doi.org\/10.1126\/science.1260419","DOI":"10.1126\/science.1260419"},{"key":"24_CR33","doi-asserted-by":"publisher","unstructured":"Van Valen, D.A., et al.: Deep learning automates the quantitative analysis of individual cells in live-cell imaging experiments. PLoS Comput. Biol. 12(11), e1005177 (2016). https:\/\/doi.org\/10.1371\/journal.pcbi.1005177","DOI":"10.1371\/journal.pcbi.1005177"},{"key":"24_CR34","doi-asserted-by":"crossref","unstructured":"Wieser, M., Siegismund, D., Heyse, S., Steigele, S.: Vision transformers show improved robustness in high-content image analysis. In: Swiss Conference on Data Science (SDS) (2022)","DOI":"10.1109\/SDS54800.2022.00021"},{"key":"24_CR35","doi-asserted-by":"crossref","unstructured":"Wieser, M., Siegismund, D., Steigele, S.: Revisiting deep archetypal analysis for phenotype discovery in high content imaging. In: IEEE\/CVF Winter Conference on Applications of Computer Vision (WACV) (2025)","DOI":"10.1109\/WACV61041.2025.00374"},{"issue":"5","key":"24_CR36","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/j.tibtech.2010.02.005","volume":"28","author":"F Zanella","year":"2010","unstructured":"Zanella, F., Lorens, J.B., Link, W.: High content screening: seeing is believing. Trends Biotechnol. 28(5), 237\u2013245 (2010). https:\/\/doi.org\/10.1016\/j.tibtech.2010.02.005","journal-title":"Trends Biotechnol."},{"key":"24_CR37","unstructured":"Zhao, X., et al.: Fast segment anything (2023). https:\/\/arxiv.org\/abs\/2306.12156"},{"issue":"2","key":"24_CR38","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.molcel.2020.05.013","volume":"79","author":"B Zuckerman","year":"2020","unstructured":"Zuckerman, B., Ron, M., Mikl, M., Segal, E., Ulitsky, I.: Gene architecture and sequence composition underpin selective dependency of nuclear export of long RNAs on NXF1 and the TREX complex. Mol. Cell 79(2), 251\u2013267 (2020). https:\/\/doi.org\/10.1016\/j.molcel.2020.05.013","journal-title":"Mol. Cell"}],"container-title":["Lecture Notes in Computer Science","Pattern Recognition"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-032-12840-9_24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T03:26:15Z","timestamp":1767324375000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-032-12840-9_24"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"ISBN":["9783032128393","9783032128409"],"references-count":38,"URL":"https:\/\/doi.org\/10.1007\/978-3-032-12840-9_24","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]},"assertion":[{"value":"2 January 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"DAGM GCPR","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"DAGM German Conference on Pattern Recognition","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Freiburg","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Germany","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2025","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"23 September 2025","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"26 September 2025","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"47","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"dagm2025","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/www.dagm-gcpr.de\/year\/2025","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}