HomePeopleResearch and SupportPublicationsNews

Publications

    arXiv and bioRxiv pre-publications:

  1. P.J. Harrison, H. Wieslander, A. Sabirsh, J. Karlsson, V. Malmsjö, A. Hellander, C. Wählby, and O. Spjuth.

    Deep learning models for lipid-nanoparticle-based drug delivery.

    https://doi.org/10.1101/2020.04.06.027672, April 2020.

  2. G. Partel and C. Wählby.

    Spage2vec: Unsupervised detection of spatial gene expression constellations.

    https://doi.org/10.1101/2020.02.12.945345, Feb 2020.

  3. G. Partel, M.M. Hilscher, G. Milli, L. Solorzano, A.H. Klemm, M. Nilsson, and C. Wählby.

    Identification of spatial compartments in tissue from in situ sequencing data.

    https://doi.org/10.1101/765842, Sept 2019.

  4. M.K. Bandaru, A. Emmanouilidou, P. Ranefall, B. von der Heyde, E. Mazzaferro, T. Klingströ, M. Masiero, O. Dethlefsen, J. Ledin, A. Larsson, H. L. Brooke, C. Wählby, E. Ingelsson, and M. den Hoed.

    Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis.

    doi: https://doi.org/10.1101/502674, March 17, 2019.

  5. G. Partel, G. Milli, and C. Wählby.

    Improving recall of in situ sequencing by self-learned features and a graphical model.

    Permanent arXiv identifier: 1802.08894, Feb 2018.

  6. reviewed publications:

  7. H. Wieslander, P. J Harrison, G. Skogberg, S. Jackson, M. Friden, J. Karlsson, O. Spjuth, and C. Wählby.

    Deep learning and conformal prediction for hierarchical analysis of large-scale whole-slide tissue images

    IEEE Journal of Biomedical and Health InformaticsBioinformatics, doi:10.1109/JBHI.2020.2996300, June 2020.

  8. L. Solorzano, G. Partel, and C. Wählby.

    TissUUmaps: Interactive visualization of large-scale spatial gene expression and tissue morphology data.

    Bioinformatics, doi:10.1093/bioinformatics/btaa541, May 2020.

  9. N. Pielawski and C. Wählby.

    Introducing Hann windows for reducing edge-effects in patch-based image segmentation.

    PLoS One 15(3):e0229839. Mar 12, 2020, doi:10.1371/journal.pone.0229839.

  10. N. Pielawski, J. Hu, S. Strömblad, and C. Wählby.

    In silico prediction of cell traction forces.

    Proc IEEE Int Symp Biomed Imaging 2020, April 2020, doi:10.1109/ISBI45749.2020.9098359

  11. A. Gupta, V. Larsson, D. Matuszewski, S. Strömblad, and C. Wählby.

    Weakly-supervised prediction of cell migration modes in confocal microscopy images using bayesian deep learning.

    Proc IEEE Int Symp Biomed Imaging 2020, April 2020, doi:10.1109/ISBI45749.2020.9098548

  12. A. Andersson, G. Partel, L. Solorzano, and C. Wählby.

    Transcriptome-supervised classification of tissue morphology using deep learning

    Proc IEEE Int Symp Biomed Imaging 2020, April 2020, doi:10.1109/ISBI45749.2020.9098361

  13. P. Ström, K. Kartasalo, H. Olsson, L. Solorzano, B. Delahunt, D.M. Berney, D.G. Bostwick, A.J. Evans, D.J. Grignon, P.A. Humphrey, K.A. Iczkowski, J.G. Kench, G. Kristiansen, T.H. van der Kwast, K.R.M. Leite, J.K. McKenney, J. Oxley, C-C. Pan, H. Samaratunga, J.R. Srigley, H. Takahashi, T. Tsuzuki, M. Varma, M. Zhou, J. Lindberg, C. Lindskog, P. Ruusuvuori, C. Wählby, H. Grönberg, M. Rantalainen, L. Egevad, and M. Eklund.

    Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study.

    Lancet Oncology, doi: 10.1016/S1470-2045(19)30738-7, Jan 8, 2020.
    The paper is mentioned in Läkartidningen.

  14. G. Günaydın, G. Edfeldt, D. A. Garber, M. Asghar, L. Noël-Romas, A. Burgener, C. Wählby, L. Wang, L. C. Rohan, P.Guenthner, J. Mitchell, N. Matoba, J. M. McNicholl, K. E. Palmer, A. Tjernlund, and K. Broliden

    Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa.

    Scientific Reports, doi: 10.1038/s41598-019-54493-4 Dec 2, 2019.

  15. A. Gupta, P.J. Harrison, H. Wieslander, N. Pielawski, K. Kartasalo, G. Partel, L. Solorzano, A. Suveer, A. H. Klemm, O. Spjuth, I-M. Sintorn, and C. Wählby.

    Deep Learning in Image Cytometry: A Review.

    Cytometry A. doi: 10.1002/cyto.a.23701, Dec 19 2018.

  16. L. Solorzano, G. M. Almeida, B. Mesquita, D. Martins, C. Oliveira, and C. Wählby.

    Whole Slide Image Registration for the Study of Tumor Heterogeneity.

    Presented at COMPAY workshop of MICCAI 2018 21st International Conference on Medical Image Computing and Computer Assisted Intervention, September 16-20 2018, Granada, Spain, published in Lecture Notes in Computer Science, Computational Pathology and Ophthalmic Medical Image Analysis; LNCS 11039, pp 95-102, Springer, Cham. doi: 10.1007/978-3-030-00949-6_12

  17. K. Holzwarth, R. Köhler, L. Philipsen, K. Tokoyoda, V. Ladyhina, C. Wählby, R.A. Niesner, and A.E. Hauser.

    Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections.

    Cytometry A 2018 Jul;93(9):876-888. doi: 10.1002/cyto.a.23526, Aug 14 2018.

  18. D.J. Matuszewski, C. Wählby, C. Krona, S. Nelander, and I-M. Sintorn.

    Image-based detection of patient-specific drug-induced cell-cycle effects in glioblastoma.

    SLAS Discovery 2018 Dec;23(10):1030-1039. doi: 10.1177/2472555218791414, Aug 3 2018.

  19. N. Schizas, S. Perry, B. Andersson, C. Wählby, K. Kullander, and N.P. Hailer.

    Differential Neuroprotective Effects of Interleukin-1 Receptor Antagonist on Spinal Cord Neurons after Excitotoxic Injury.

    Neuroimmunomodulation 2017;24(4-5):220-230. doi: 10.1159/000484607, Jan 2018.

  20. A. Gibbs, M. Buggert, G. Edfeldt, P. Ranefall, A. Introini, S. Cheuk, E. Martini, L. Eidsmo, T.B. Ball, J. Kimani, R. Kaul, A. Karlsson, C. Wählby, K. Broliden, and A. Tjernlund.

    HIV-infected women have high numbers of CD103-CD8+ T cells residing close to the basal membrane of the ectocervical epithelium.

    Journal of Infectious Diseases 2018 Jul 2;218(3):453-465. doi: 10.1093/infdis/jix661, Dec 2017. Note; this paper also made it to the journal cover.

  21. D.J. Matuszewski, A. Hast, C. Wählby, and I.-M. Sintorn

    A short feature vector for image matching: The Log-Polar Magnitude feature descriptor.

    PLoS One 2017 Nov 30;12(11) doi: 10.1371/journal.pone.0188496, Nov 2017.

  22. J. Carreras-Puigvert, M. Zitnik, A.-S. Jemth, M. Carter, J.E. Unterlass, B. Hallström, O. Loseva, Z. Karem, J.M. Calderon-Montano, C. Lindskog, P.-H. Edqvist, D.J. Matuszewski, H. Ait Blal, R.P.A. Berntsson, M. Häggblad, U. Martens, M. Studham, B. Lundgren, C. Wählby, E.L.L. Sonnhammer, E. Lundberg, P. Stenmark, B. Zupan, and T. Helleday.

    A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family.

    Nature Communications 2017 Nov 16;8(1):1541. doi:10.1038/s41467-017-01642-w, Nov 2017.

  23. H. Zhang, M. Ericsson, M. Virtanen, S. Weström, C. Wählby, A. Vahlquist and H. Törmä.

    Quantitative image analysis of protein expression and colocalization in skin sections

    Experimental Dermatology 2018 Feb;27(2):196-199. doi: 10.1111/exd.13457, Nov 2017.

  24. M. Bombrun, H. Gao, P. Ranefall, N. Mejhert, P. Arner and C. Wählby.

    Quantitative high-content/high-throughput microscopy analysis of lipid droplets in subject-specific adipogenesis models

    Cytometry A 2017 Nov;91(11):1068-1077. doi: 10.1002/cyto.a.23265, Oct 2017. Note; this paper also made it to the journal cover.

  25. H. Wieslander, G. Forslid, E. Bengtsson, C. Wählby, J.-M. Hirsch, C. Runow Stark and S.K. Sadanandan.

    Deep Convolutional Neural Networks For Detecting Cellular Changes Due To Malignancy

    Proceedings of the IEEE International Conference on Computer Vision (ICCV), Bioimage Computing Workshop, pp. 82-89, 2017, Venice, Oct 2017.

  26. S.K. Sadanandan, K. Karlsson and C. Wählby.

    Spheroid Segmentation Using Multiscale Deep Adversarial Networks

    Proceedings of the IEEE International Conference on Computer Vision (ICCV), Bioimage Computing Workshop, pp. 36-41, 2017, Venice, Oct 2017.

  27. S.K. Sadanandan, P. Ranefall, S. Le Guyader and C. Wählby.

    Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

    Nature Scientific Reports 7:7860 doi:10.1038/s41598-017-07599-6, August 2017.

  28. M. Bombrun, P. Ranefall, J. Lindblad, A. Allalou, G. Partel, L. Solorzano, X. Qian, M. Nilsson, and C. Wählby.

    Decoding Gene Expression in 2D and 3D.

    Presented at SCIA17 (Scandinavian Conference on Image Analysis), Tromsö, Norway, June 12-14, 2017, published in Lecture Notes in Computer Science; LNCS 10270: 257-268. Springer, Cham.

  29. N. Talebizadeh, N.Z. Hagströom, Z. Yu, M. Kronschläger, P. Söderberg and C. Wählby.

    Objective Automated Quantification ofFluorescence Signal in Histological Sectionsof Rat Lens

    Cytometry A doi: 10.1002/cyto.a.23131, May 2017.

  30. S.K. Sadanandan, P. Ranefall, and C. Wählby.

    Feature Augmented Deep Neural Networks for Segmentation of Cells.

    Lecture Notes in Computer Science Computer Vision - ECCV 2016 Workshops, Volume 9913, pp 231-243, Sept 2016.

  31. O. Ishaq, S.K. Sadanandan, and C. Wählby.

    Deep Fish: Deep Learning-Based Classification of Zebrafish Deformation for High-Throughput Screening.

    Journal of Biomolecular Screening / SLAS Discovery 22(1):102-107 doi:10.1177/1087057116667894, Jan 2017.

  32. C. Wählby.

    The quest for multiplexed spatially resolved transcriptional profiling.

    Nature Methods 13(8), 623-624 doi:10.1038/nmeth.3924, July 2016.

  33. M. Mignardi, O. Ishaq, X. Qian, and C. Wählby.

    Bridging Histology and Bioinformatics - Computational Analysis of Spatially Resolved Transcriptomics.

    Proceedings of the IEEE 99, doi: 10.1109/JPROC.2016.2538562, April 2016.

  34. D. J. Matuszewski, C. Wählby, J. C. Puigvert, and I-M. Sintorn.

    PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data.

    PLoS ONE 17;11(3):e0151554. doi: 10.1371/journal.pone.0151554, March 2016.

  35. P. Ranefall and C. Wählby.

    Global gray-level thresholding based on object size.

    Cytometry A, 89(4):385-90. DOI: 10.1002/cyto.a.22806, April 2016.

  36. C. Wählby.

    Image Segmentation, Processing and Analysis in Microscopy and Life Science.

    Book chapter, pages 1-16, in Mathematical Models in Biology: Bringing Mathematics to Life, Springer December 2015, Editors: V. Zazzu, M.B. Ferraro and M.R. Guarracino, ISBN 978-3-319-23496-0.

  37. S.K. Sadanandan, Ö. Baltekin, K.E.G. Magnusson, A. Boucharin, P. Ranefall, J. Jaldén, J. Elf, and C. Wählby.

    Segmentation and track-analysis in time-lapse imaging of bacteria.

    IEEE Journal of Selected Topics in Signal Processing, October 15, 2015, 10(1):174-184

  38. C.-M. Clausson, L. Arngården, O. Ishaq, A. Klaesson, M. Kühnemund, K. Grannas, B. Koos, X. Qian, P. Ranefall, T. Krzywkowski, H. Brismar, M. Nilsson, C. Wählby and O. Söderberg.

    Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio.

    Nature Scientific Reports 5, 12317, June 2015, doi:10.1038/srep12317.

  39. B. Koos, M. Kamali-Moghaddam, L. David, M Sobrinho-Simões, A. Dimberg, M. Nilsson, C. Wählby, and O. Söderberg.

    Next generation Pathology - surveillance of tumor microecology.

    J Mol Biol., 2015 June 5, 427(11):2013-22, doi: 10.1016/j.jmb.2015.02.017.
    Ranked number two as most downloaded in August 2015.

  40. O. Ishaq, J. Elf, and C. Wählby

    An evaluation of the faster STORM method for super-resolution microscopy.

    Proc IEEE ICPR 2014, 22nd International Conference on Pattern Recognition, August 24-28, 2014, Stockholm, Sweden.

  41. A. Pacureanu, R. Ke, M. Mignardi, M. Nilsson, and C. Wählby.

    Image based in situ sequencing for RNA analysis in tissue.

    Proc IEEE ISBI 2014, International Society of Biomedical Imaging, 29 April - 2 May, 2014, Beijing, China.

  42. C. Wählby, A.L. Conery, M.A. Bray, L. Kamentsky, J Larkins-Ford, KL Sokolnicki, M Veneskey, K Michaels, A.E. Carpenter, and E.J. O'Rourke.

    High- and low-throughput scoring of fat mass and body fat distribution in C. elegans.

    Methods, 2014 Aug 1;68(3):492-9. doi: 10.1016/j.ymeth.2014.04.017. PMID: 24784529

  43. M.A. Khorshidi, P.K. Periyannan Rajeswari, C. Wählby, H.N. Joensson, and H. Andersson Svahn.

    Automated analysis of dynamic behavior of single cells in picoliter droplets.

    Lab on a Chip, 2014 (14), 931-937. doi: 10.1039/c3lc51136g. PMID: 24385254

  44. R. Ke, M. Mignardi, A. Pacureanu, J. Svedlund, J. Botling, C. Wählby, and M. Nilsson.

    In situ sequencing for RNA analysis in preserved tissue and cells.

    Nature Methods, 2013 (10), 857-860. doi: 10.1038/nmeth.2563. PMID: 23852452

  45. N.V. Kirienko, D.R. Kirienko,J. Larkins-Ford, C. Wählby, G. Ruvkun, and F.M. Ausubel.

    Pseudomonas aeruginosa disrupts Caenorhabditis elegans iron homeostasis, causing a hypoxic response and death.

    Cell Host and Microbe, 2013 Apr 17;13(4):406-16. doi: 10.1016/j.chom.2013.03.003.

  46. C. Pardo-Martin, A. Allalou, J. Medina, P.M. Eimon, C. Wählby, and M.F. Yanik.

    High-throughput hyperdimensional vertebrate phenotyping.

    Nature Communications, 2013 Feb 12; 4:1467, doi:10.1038/ncomms2475, PMID: 23403568
    Also featured here!

  47. M. Gavrilovic, J.C. Azar, J. Lindblad, C. Wählby, E. Bengtsson, C. Busch, and I.B. Carlbom.

    Blind color decomposition of histological images.

    IEEE Transactions on Medical Imaging, 2013 Jun; 32(6):983-94. doi: 10.1109/TMI.2013.2239655. PMID: 23322760

  48. O. Ishaq, J. Negri, M.-A. Bray, A. Pacureanu, R.T. Peterson, and C. Wählby.

    Automated Quantification of zebrafish tail deformation for high-throughput drug screening.

    Proc IEEE Int Symp Biomed Imaging 2013; 902-905. doi: 10.1109/ISBI.2013.6556621. PMCID: PMC3909804

  49. A.K. Raap, R.S. Jahangir Tafrechi, F.M. van de Rijke, A. Pyle, C. Wählby, K. Szuhai, R.B.G. Ravelli, R.F.M. de Coo, H.K. Rajasimha, M. Nilsson, P.F. Chinnery, D.C. Samuels, and G.M.C. Janssen.

    Non-random mtDNA segregation patterns indicate a metastable heteroplasmic segregation unit in m.3243A>G cybrid cells.

    PLos One, 2012 Dec 18; Epub ahead of print. doi: 10.1371/journal.pone.0052080. PMID: 23272214 [pdf]

  50. S.I. Niwas, A. Kårsnäs, V. Uhlmann, P. Palanisamy, C. Kampf, M. Simonsson, C. Wählby, and R. Strand.

    Automated classification of immunostaining patterns in breast tissue from the Human Protein Atlas

    Journal of Pathology Informatics, 2013 Mar 30;4(Suppl):S14. doi: 10.4103/2153-3539.109881 Also presented at MICCAI 2012 workshop on Histopathology Image Analysis (HIMA): Image Computing in Digital Pathology, Nice, October 2012.

  51. C. Wählby, L. Kamentsky L, Z.H. Liu, T. Riklin-Raviv, A.L. Conery, E.J. O'Rourke, K.L. Sokolnicki, O. Visvikis, V. Ljosa, J.E. Irazoqui, P. Golland, G. Ruvkun G, F.M. Ausubel, and A. E. Carpenter.

    An image analysis toolbox for high-throughput C. elegans assays.

    Nature Methods, 2012 Apr 22; 9(7): 714-716. doi: 10.1038/nmeth.1984 PMID: 22522656 [NIH Public access version.]

    Also featured here!
  52. T.Y. Chang, C. Pardo-Martin, A. Allalou, C. Wählby and M.F. Yanik.

    Fully automated cellular-resolution vertebrate screening platform with parallel animal processing.

    Lab on a Chip, 2012 Feb 21;12(4):711-6 PMID: 22159032 []

  53. C-M. Clausson, A. Allalou, I. Weibrecht, S. Mahmoudi, M. Farnebo, U. Landegren, C. Wählby and O. Söderberg.

    Increasing the dynamic range of in situ PLA.

    Nature Methods, 2011 Oct 28;8(11):892-3. doi: 10.1038/nmeth.1743 PMID: 22036742 []

  54. I. Weibrecht, M. Gavrilovic, L. Lindbom, U. Landegren, C.Wählby and O. Söderberg.

    Visualising individual sequence-specific protein-DNA interactions in situ.

    New Biotechnology, 2012 Jun 15;29(5):589-98. doi: 2011 doi:10.1016/j.nbt.2011.08.002 PMID: 21906700 []

  55. M. Gavrilovic, I. Weibrecht, T. Conze, O. Söderberg and C.Wählby.

    Automated Classification of Multi-Colored Rolling Circle Products in Dual-channel Wide-field Fluorescence Microscopy.

    Cytometry A. 2011 Jun 10. doi: 10.1002/cyto.a.21087. PMID:21671402 [pdf]

  56. T. Riklin Raviv, V. Ljosa, A.L. Conery, F.M. Ausubel, A.E. Carpenter, P. Golland and C. Wählby.

    Morphology-Guided Graph Search for Untangling Objects: C. elegans Analysis.

    Med Image Comput Comput Assist Interv. 2010;13(Pt 3):634-41. PMID:20879454 [pdf]

  57. C. Wählby, T. Riklin-Raviv, V. Ljosa, A.L. Conery, P. Golland, F.M. Ausubel, and A.E. Carpenter.

    Resolving clustered worms via probabilistic shape models.

    Proc IEEE Int Symp Biomed Imaging. 2010 Jun 21;2010(14-17 April 2010):552-555. PMID:21383863 [pdf]

  58. A. Zieba, C. Wählby, F. Hjälm, L. Jordan, J. Berg, U. Landegren, K. Pardali.

    Bright-field microscopic visualization of proteins and protein complexes by in situ proximity ligation with peroxidase detection.

    Clinical Chemistry. 2010 Jan;56(1):99-110. PMID:19926775 [pdf]

  59. M. Gavrilovic and C. Wählby.

    Suppression of Autofluorescence based on Fuzzy Classification by Spectral Angles.

    Presented at MICCAI 2009, the 12th International Conference on Medical Image Computing and Computer Assisted Intervention, Workshop on Optical Tissue Image analysis in Microscopy, Histopathology and Endoscopy, September 20-24, Imperial College London, UK, 2009, pp135-146. [pdf]

  60. A . Allalou, A. Pinidiyaarachchi, C. Wählby.

    Robust signal detection in 3D fluorescence microscopy.

    Cytometry A. 2009 Sep; 77A(1):86-96. PMID: 19760746 [pdf]

  61. M. Gavrilovic and C. Wählby.

    Quantification of colocalization and cross-talk based on spectral angles.

    J Microsc. 2009 Jun;234(3):311-24.PMID: 19493110 [pdf]

  62. A. Pinidiyaarachchi, A. Allalou, A. Zieba, K. Pardali and C. Wählby.

    A detailed analysis of 3D subcellular signal localization.

    Cytometry A. 2009 Apr; 75(4):319-28.PMID: 19006073 [pdf]

  63. J. Göransson, C. Wählby, M. Isaksson, M. Howell, J. Jarvius and M. Nilsson.

    A single molecule array for digital targeted molecular analyses.

    Nucleic Acids Res. 2009 Jan;37(1):e7. Epub 2008 Nov 25. PMID: 19033366 [pdf]

  64. A. Allalou and C. Wählby.

    BlobFinder; a tool for fluorescence microscopy image cytometry.

    Computer Methods and Programs in Biomedicine, 2009 Apr;94(1):58-65. Epub 2008 Oct 23. [pdf]

  65. C. Wählby, P. Karlsson, S. Henriksson, C. Larsson, M. Nilsson and E. Bengtsson.

    Finding cells, finding molecules, finding patterns.

    Int. J. of Signal and Imaging Systems Engineering (IJSISE), 1(1):11-17,2008. [pdf]

  66. R.S. Jahangir Tafrechi, F.M. van de Rijke, A. Allallou, C. Larsson, W.C.R. Sloos, M. van de Sande, C. Wählby, G.M.C. Janssen, and A.K. Raap.

    Single-cell A3243G Mitochondrial DNA Mutation Load Assays for Segregation Analysis.

    J. of Histochemistry and Cytochemistry, 55: 1159-1166, Nov 2007. PMID: 17679731 [pdf]

  67. A. Allalou, F.M. van de Rijke, R. Jahangir Tafrechi, A.K. Raap, and C. Wählby.

    Image based measurements of single cell mtDNA mutation load.

    Presented at SCIA07 (Scandinavian Conference on Image Analysis), Aalborg, June 10-14, 2007, published in Lecture Notes in Computer Science; LNCS 4522: 631-640, Springer, 2007. [pdf]

  68. M. Jarvius, J. Paulsson, I. Weibrecht, K-J. Leuchowius, A-C. Andersson, C. Wählby, M. Gullberg, J. Botling, T. Sjöblom, B. Markova, A. östman, U. Landegren and O. Söderberg.

    In situ detection of phosphorylated PDGF receptor beta using a generalized proximity ligation method.

    Molecular and Cellular Proteomics, 6:1500-1509, 2007. PMID: 17565975 [pdf]

  69. K. Althoff, J. Degerman, C. Wählby, T. Thorlin, J. Faijerson, R. S. Eriksson, and T. Gustavsson.

    Time-Lapse Microscopy and Classification of in Vitro Cell Migration Using Hidden Markov Modeling.

    ICASSP 2006, published on line in IEEE Xplore; IEEE International Conference on Acoustics, Speech and Signal Processing, Tolouse, France, May 2006. [pdf]

  70. A. Pinidiyaarachchi and C. Wählby.

    Seeded watersheds for combined segmentation and tracking of cells.

    Presented at ICIAP 2005 (International Conference on Image Analysis and Processing) in Cagliari, Italy, September 6-8, 2005. Published in Lecture Notes in Computer Science, LNCS 3617: 336-343, Springer, 2005. [pdf]

  71. P. Holting and C. Wählby.

    Easy-to-use object selection by color space projections and watershed segmentation.

    Presented at ICIAP 2005 (International Conference on Image Analysis and Processing) in Cagliari, Italy, September 6-8, 2005. Published in Lecture Notes in Computer Science, LNCS 3617: 269-276, Springer, 2005. [pdf]

  72. E. Bengtsson, C. Wählby and J. Lindblad.

    Robust cell image segmentation methods.

    Pattern Recognition and Image Analysis 14(2):157-167, 2004. [pdf]

  73. C. Wählby, I.-M. Sintorn, F. Erlandsson, G. Borgefors and E. Bengtsson.

    Combining intensity, edge, and shape information for 2D and 3D segmentation of cell nuclei in tissue sections.

    Journal of Microscopy, 215(1):67-76, July 2004. PMID: 15230877 [pdf]

  74. J. Lindblad, C. Wählby, E. Bengtsson and A. Zaltsman.

    Image analysis for automatic segmentation of cells and classification of Rac1 activation.

    Cytometry, 57A(1):22-33, 2004. PMID: 14699602 [pdf]

  75. F. Erlandsson, C. Wählby, S. Ekholm-Reed, A-C. Hellström, E. Bengtsson and A. Zetterberg.

    Abnormal expression of cyclin E in tumor cells.

    International Journal of Cancer, 104(3):369-75, Apr 1, 2003. PMID: 12569561 [pdf]

  76. C. Wählby and Ewert Bengtsson.

    Segmentation of Cell Nuclei in Tissue by Combining Watersheds with Gradient Information.

    Presented at SCIA-03 (Scandinavian Conference on Image Analysis), Gothenburg, Sweden, July 2003. Published in Lecture Notes in Computer Science, LNCS 2749: 408-414, 2003. [pdf]

  77. C. Wählby, J. Lindblad, M. Vondrus, E. Bengtsson and L. Björkesten.

    Algorithms for cytoplasm segmentation of fluorescence labeled cells.

    Analytical Cellular Pathology, 24(2,3):101-111, 2002. PMID: 12446959 [pdf]

  78. C. Wählby, F. Erlandsson, A. Zetterberg, and E. Bengtsson.

    Sequential immunofluorescence staining and image analysis for detection of large numbers of antigens in individual cell nuclei.

    Cytometry, 47(1):32-41, 2002. PMID: 11774347 [pdf]

  79. C. Wählby, F. Erlandsson, K. Nyberg, J. Lindblad, A. Zetterberg, and E. Bengtsson.

    Multiple antigen analysis by sequential immunofluorescence staining and multi-dimensional image analysis.

    Proceedings of SCIA-01 (Scandinavian Conference on Image Analysis), Bergen, Norway, June 2001. p. 25-31. [pdf]

  80. F. Erlandsson, C. Linnman(=Wählby), S. Ekholm, E. Bengtsson, and A. Zetterberg.

    A detailed analysis of cyclin A accumulation at the G1/S border in normal and transformed cells.

    Experimental Cell Research 256:86-95, 2000. PMID: 10942581 [pdf]

  81. H. Söderqvist, G. Imreh, M. Kihlmark, C. Linnman(=Wählby), N. Ringertz, and E. Hallberg.

    Intra cellular distribution of an integral nuclear pore membrane protein fused to green fluorescent protein: Localization of a targeting domain.

    European Journal of Biochemistry 250:808-813, 1997. PMID: 9461306 [pdf]

PhD thesis

Patent

  • C. Wählby, M. Gavrilovic, E. Bengtsson, J. Lindblad.

    "Pixel Classification in Image Analysis"

    North American patent pending, filed August 2009.

Other conference presentations and invited talks

  • C. Wählby

    Image based drug discovery - challenges and opportunities at the microscopy scale.

    Invited speaker at the 19th Scandinavian Conference on Image Analysis, at the IT University of Copenhagen in Denmark, June 2015.

  • C. Wählby

    Characterizing solid tumors by image-based high throughput screening of cancer stem cells.

    Invited speaker at the 2nd High Throughput Cell Biology: from screening to applications, at Institut Curie - Research Centre, Paris, France, November 2014.

  • C. Wählby

    Image processing and analysis in microscopy and life science.

    Invited speaker on mathematics and biology at the BMTL meeting in Naples, Italy, October 2014.

  • C. Wählby

    Combining image-based in situ RNA screening with quantitative analysis of cell and tissue morphology.

    Invited speaker at the 1st annual conference for the Society of Biomolecular Imaging and Informatics SBI2, at the JB Martin Conference Center at Harvard Medical School, Boston, MA, USA, September 2014. Carolina Wählby was honored with the 'SBI2 President's innovation award' for her presentation.

  • C. Wählby

    Quantitative microscopy: extracting relevant information from biomedical image data.

    Invited speaker at the International Microscopy Congress (IMC) in Prague, Czech Republic, September 2014.

  • C. Wählby

    Extracting discoveries hidden in images.

    Invited speaker at the international conferenceon Advances in Tissue Regeneration in Lattorp, the Netherlands, November 2013.

  • A. Pacureanu, F. Peyrin, M. Langer, O. Ishaq, A. Allalou, and C. Wählby

    Isotropic 3D imaging of biological specimens at micro and nano scale.

    Oral presentation by A. Pacureanu at BSRT - The Show of Regeneration, Berlin, Germany, December 5 - 7, 2012.

  • C. Wählby

    High throughput screening for novel anitinfectives using model organisms.

    Poster at conference on 'Joint battle against infectious disease and antimicrobial resistance', Uppsala, Sweden, November 23, 2012.

  • C. Wählby

    High throughput phenotyping of model organisms.

    Invited speaker at Bioimage Informatics, Dresden, Germany, September 16 - 19, 2012.

  • A. Pacureanu, O. Ishaq, A. Allalou, and C. Wählby

    Making isotropic 3D imaging at microscopic scale accessible to every lab.

    Oral presentation by A. Pacureanu at Bioimage Informatics, Dresden, Germany, September 16 - 19, 2012.

  • M. Simonsson, A.T. Bayrak, and C. Wählby

    Optimization of semi-automated cell tracking using application-expert feed-back.

    Poster presentation by M. Simonsson at Bioimage Informatics, Dresden, Germany, September 16 - 19, 2012.

  • O. Ishaq, J. Negri, M.-A. Bray, A. Pacureanu, and C. Wählby

    An image based high-throughput assay for chemical screening on using zebrafish.

    Poster presentation by O. Ishaq at Bioimage Informatics, Dresden, Germany, September 16 - 19, 2012.

  • C. Wählby

    Quantitative Microscopy; from drug discovery in model organisms to in situ RNA sequencing.

    Poster at SciLifeLab Day, Uppsala, Sweden, August 23, 2012.

  • C. Wählby

    A toolbox for high-throughput C. elegans phenotyping.

    Invited speaker at the Automated Imaging & High-Throughput Phenotyping conference at Cold Spring Harbour Laboratory, NY, USA, April 10 - 13, 2012.

  • C. Wählby

    The WormToolbox: automated image analysis for high-throughput C. elegans assays.

    Invited speaker at the 2012 NordForsk C. elegans network meeting in Sigtuna, Sweden, March 2 - 4, 2012.

  • C. Wählby, L. Kamentsky, K.L. Madden and A.E. Carpenter

    Quantifying phenotypic variation in image-based C. elegans screens.

    Poster presentation at the BioImage Informatics II conference at Janelia Farm, MD, USA, Sept 18-21, 2011.

  • C. Wählby

    Image based, high-throughput screening of gene function in cells and model organisms.

    Invited speaker at conference on 'Putting proteins under the microscope; future PROSPECTS for biological imaging.' The Karolinska Instutute, Stockholm, August 24, 2011

  • C. Wählby, L. Kamentsky, Z.H. Liu, T. Riklin-Raviv, A.L. Conery, E.J. O'Rourke, K.L. Madden, O. Visviks, V. Ljosa, J.E. Irazoqui, P. Golland, G. Ruvkun, F.M. Ausubel and A.E. Carpenter

    A novel, high-throughput, liquid killing assay of P. aeruginosa infection of C.elegans provides insight about pathogenesis and host defense.

    Oral presentation at the 18th International C. elegans Meeting, University of California, Los Angeles, June 22 - June 26, 2011.

  • N.V. Kirienko, J. Larkins-Ford,C. Wählby and F. M. Ausubel

    The WormToolbox: automated quantification of image C.elegans phenotypes.

    Poster presentation at the 18th International C. elegans Meeting, University of California, Los Angeles, June 22 - June 26, 2011.

  • A. Allalou, V. Curic, C. Pardo-Martin, M.F. Yanik and C. Wählby.

    Approaches for increasing throughput and information content of image-based zebrafish screens

    in Proc. of Swedish Symposium in Image Analysis (SSBA) 2011, Linköping, Sweden, March 2011.

  • C. Wählby, Z. H. Liu, T. Riklin-Raviv, L. Kamentsky, K. Madden, V. Ljosa, A.L. Conery, E. O'Rourke, N. Kirienko, Orane Visvikis, A. Fraser, J.E. Irazoqui, P. Golland , G. Ruvkun, F.M. Ausubel and A.E. Carpenter.

    Image-based high-throughput screening using C. elegans

    Poster presentation at the Cold Spring Harbor conference on Automated Imaging and High-Throughput Phenotyping, Cold Spring Harbor, NY, USA, Dec 5-8, 2010.

  • C. Wählby

    Improving the toolbox for high throughput screening on neurons

    Poster presentation at the What Can Computer Vision Do for Neuroscience and Vice Versa? conference at Janelia Farm, MD, USA, Nov 14-17, 2010.

  • C. Wählby, T. Riklin-Raviv, V. Ljosa, A.L. Conery, P. Golland , F.M. Ausubel and A.E. Carpenter.

    Image-based high-throughput screening using C. elegans

    Oral presentation at the Bioimage Informatics 2010 conference, Carnegi Mellon, Pittsburgh, USA, Sept 17-19, 2010.

  • C. Wählby, Z. H. Liu, T. Riklin-Raviv, L. Kamentsky, K. Madden, V. Ljosa, A.L. Conery, E. O'Rourke, J.E. Irazoqui, P. Golland , F.M. Ausubel and A.E. Carpenter.

    Image-based high-throughput screening using C. elegans

    Poster presentation at the Broad Institute Sixth Annual Retreat, Harvard Medical School, Boston, MA, USA, Nov 8-9, 2010.

  • C. Wählby.

    Digital Image Analysis of Cells: Informatics & Knowledge Extraction.

    Invited plenary speaker of CYTO 2010: XXV Congress of the International Society for Advancement of Cytometry, Seattle, Washington, USA, May 8-12, 2010.

  • C. Wählby.

    Quantification of colocalization and cross-talk based on spectral angles - the story about the angle histogram.

    Invited speaker at MIT Computer Science and Artificial Intelligence Laboratory (CSAIL), Cambridge, MA, USA, February 25,2010.

  • M. Gavrilovic, C. Wählby, J. Lindblad, E. Bengtsson.

    Spectral Angle Histogram: a Novel Image Analysis Tool for Quantification of Colocalization and Cross-talk

    in Proc. of the 9th European Light Microscopy Initiative (ELMI) meeting, pp. 66-67, Glasgow, UK, June 2009.

  • M. Gavrilovic, C. Wählby, J. Lindblad, E. Bengtsson.

    Dimensionality Reduction for Colour Based Pixel Classification

    in Proc. of Swedish Symposium in Image Analysis (SSBA) 2009, Halmstad, Sweden, March 2009.

  • M. Gavrilovic, C. Wählby, J. Lindblad, E. Bengtsson.

    Algorithms for cross-talk suppression in fluorescence microscopy

    in Abstracts of Medicinteknikdagarna 2008, pp.64, Gothenburg, Sweden, October 2008.

  • C. Wählby.

    Image analysis in fluorescence microscopy; the human eye is not enough.

    Invited speaker, in Abstracts of Medicinteknikdagarna 2008, Gothenburg, Sweden, October 2008.

  • M. Gavrilovic and C. Wählby.

    Quantification and localization of colocalization.

    Presented at SSBA07, conference for the Swedish Society for Image Analysis, Linköping, March 2007.

  • A. Pinidiyaarachchi and C. Wählby.

    On color spaces for cytology.

    Presented at SSBA07, conference for the Swedish Society for Image Analysis, Linköping, March 2007.

  • A. Allalou, C. Wählby, F.M. van de Rijke, R. Jahangir Tafrechi, and A.K. Raap.

    Segmentation of cytoplasms of cultured cells.

    Presented at SSBA07, conference for the Swedish Society for Image Analysis, Linköping, March 2007.

  • A. Pinidiyaarachchi, J. Göransson, C. Gonzalez-Rey, M. Howell, J. Melin, J. Jarvius, M. Nilsson, E. Bengtsson, C. Wählby.

    Digital image processing for multiplexing of Single molecule detection.

    Medicinteknikdagarna Stockholm/Södertälje September 27-28, 2005

  • C. Wählby, P. Karlsson, T. Thorlin, K. Althoff, J. Degerman, E. Bengtsson, and T. Gustavsson.

    Time-lapse microscopy and image analysis for tracking stem cell migration.

    Oral presentation at the Swedish Symposium on Image Analysis, the Ångström laboratory, Uppsala, March 11-12, 2004.

  • J. Degerman, K. Althoff, T. Thorlin, C. Wählby, P. Karlsson, E. Bengtsson, and T. Gustavsson.

    Modeling stem cell migration by Hidden Markov.

    The Swedish Symposium on Image Analysis, the Ångström laboratory, Uppsala, March 11-12, 2004.

  • P. Karlsson, J. Lindblad and C. Wählby.

    Segmentation of point like fluorescent markers.

    The Swedish Symposium on Image Analysis, the Ångström laboratory, Uppsala, March 11-12, 2004.

  • C. Wählby, I. Nyström, and E. Bengtsson.

    Robust methods for image segmentation and measurements.

    Invited speaker at a conference on Modern Methods for Quantitative Metallography, Wenner Gren Center, Stockholm, November 5-6, 2003.

  • C. Wählby and E. Bengtsson.

    Watershed techniques for segmentation in image cytometry.

    Poster presentation at the 1st International Cytomics Conference, The Celtic Manor Resort, Coldra Woods, Newport, Wales, United Kingdom, May 5-9, 2003.

  • C. Wählby, F. Erlandsson, J. Lindblad, A. Zetterberg and E. Bengtsson.

    Analysis of cells using image data from sequential immunofluorescence staining experiments.

    Proceedings of 5th Korean-German joint workshop on Advanced Medical Image Processing, Seoul, May 15-18, 2001.

  • J. Lindblad, C. Wählby, M. Vondrus, E. Bengtsson, L. Björkesten.

    Statistical quality control for segmentation of fluorescence labeled cells.

    Proceedings of 5th Korean-German joint workshop on Advanced Medical Image Processing, Seoul, May 15-18, 2001.

  • C. Wählby, F. Erlandsson, A. Zetterberg and E. Bengtsson.

    Multi-dimensional image analysis of sequential immunofluorescence staining.

    Abstract, 7th ESACP Congress in Caen, April 1-5, 2001, p. 61.

  • F. Erlandsson, C. Wählby, E. Bengtsson, and A.Zetterberg.

    Detection of large numbers of antigens using sequential immunofluorescence staining.

    Abstract, 7th ESACP Congress in Caen, April 1-5, 2001, p. 56-57.

  • C. Linnman-Wählby, J. Lindblad, M. Vondrus, T. Jarkrans, E. Bengtsson and L. Björkesten.

    Automatic cytoplasm segmentation of fluorescence labelled cells.

    Proceedings, SSAB Symposium on Image Analysis, March 7-8, 2000, Halmstad, p. 29-32.

  • C. Linnman-Wählby, J. Lindblad, M. Vondrus, T. Jarkrans, E. Bengtsson and L. Björkesten.

    Algorithms for cytoplasm segmentation of fluorescence labeled cells grown in micro-fabricated structures.

    Poster presentation, Amersham Pharmacia Biotech Uppsala R&D day, December 2, 1999.

  • C. Linnman-Wählby, E. Bengtsson, S. Ekholm-Jensen, and A. Zetterberg.

    Detection of fluorescent foci and evaluation of spatial relationships in 3D-fluorescence microscopy images of mammalian cells.

    Abstract, 6th ESACP Congress in Heidelberg, April 7-11, 1999, p. 36-37.

  • C. Linnman-Wählby, and E. Bengtsson.

    Detection of fluorescent foci and evaluation of spatial relationships in 3D-fluorescence microscopy images of mammalian cells.

    Proceedings, SSAB Symposium on Image Analysis, March 9-10, 1999, Gothenburg, p. 57-60.