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  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. C. Wählby.

    The quest for multiplexed spatially resolved transcriptional profiling.

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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!

  20. 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

  21. 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

  22. 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]

  23. 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.

  24. 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!
  25. 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 []

  26. 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 [pdf]

  27. 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 [pdf]

  28. 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]

  29. 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]

  30. 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]

  31. 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]

  32. 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]

  33. A . Allalou, A. Pinidiyaarachchi, C. Wählby.

    Robust signal detection in 3D fluorescence microscopy.

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

  34. 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]

  35. 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]

  36. 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]

  37. 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]

  38. 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]

  39. 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]

  40. 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]

  41. 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]

  42. 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]

  43. 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]

  44. 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]

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

    Robust cell image segmentation methods.

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

  46. 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]

  47. 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]

  48. 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]

  49. 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]

  50. 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]

  51. 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]

  52. 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]

  53. 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]

  54. 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]

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