PUBLICATIONS BY CAROLINA WÄHLBY

1. 

   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, A. E. Carpenter

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

   Nature Methods, 2012 Apr 22 ;Epub ahead of print. doi: 10.1038/nmeth.1984 []

2. 

   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 []

3. 

   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 [pdf]

4. 

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

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

   New Biotechnology, 2011 doi:10.1016/j.nbt.2011.08.002 [pdf]

5. 

   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]

6. 

   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]

7. 

   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]

8. 

   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]

9. 

   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]

10. 

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

    Robust signal detection in 3D fluorescence microscopy.

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

11. 

    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]

12. 

    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]

13. 

    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]

14. 

    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]

15. 

    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]

16. 

    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]

17. 

    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]

18. 

    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]

19. 

    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]

20. 

    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]

21. 

    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]

22. 

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

    Robust cell image segmentation methods. Pattern Recognition and Image Analysis 14(2):157-167, 2004. [pdf]

23. 

    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]

24. 

    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]

25. 

    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]

26. 

    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]

27. 

    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]

28. 

    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]

29. 

    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]

30. 

    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]

31. 

    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

• 

  PhD in Image Analysis at Uppsala University, Sweden. PhD thesis title: Algorithms for Applied Digital Image Cytometry available at http://uu.diva-portal.org/smash/record.jsf?pid=diva2:163446

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

  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.