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Items: 1 to 50 of 124

1.

Quantitative error prediction of medical image registration using regression forests.

Sokooti H, Saygili G, Glocker B, Lelieveldt BPF, Staring M.

Med Image Anal. 2019 May 11;56:110-121. doi: 10.1016/j.media.2019.05.005. [Epub ahead of print]

PMID:
31226661
2.

Quantification of aortic pulse wave velocity from a population based cohort: a fully automatic method.

Shahzad R, Shankar A, Amier R, Nijveldt R, Westenberg JJM, de Roos A, Lelieveldt BPF, van der Geest RJ; Heart Brain Connection study group.

J Cardiovasc Magn Reson. 2019 May 13;21(1):27. doi: 10.1186/s12968-019-0530-y.

3.

CyTOFmerge: Integrating mass cytometry data across multiple panels.

Abdelaal T, Höllt T, van Unen V, Lelieveldt BPF, Koning F, Reinders MJT, Mahfouz A.

Bioinformatics. 2019 Mar 15. pii: btz180. doi: 10.1093/bioinformatics/btz180. [Epub ahead of print]

PMID:
30874801
4.

Erratum to: Automatic quantification of bone marrow edema on MRI of the wrist in patients with early arthritis: A feasibility study (Magn Reson Med. 2018; 79:1127-1134).

Aizenberg E, Roex EAH, Nieuwenhuis WP, Mangnus L, van der Helm-van Mil AHM, Reijnierse M, Bloem JL, Lelieveldt BPF, Stoel BC.

Magn Reson Med. 2019 Jul;82(1):510. doi: 10.1002/mrm.27698. Epub 2019 Feb 8. No abstract available.

PMID:
30786047
5.

An efficient preconditioner for stochastic gradient descent optimization of image registration.

Qiao Y, Lelieveldt BPF, Staring M.

IEEE Trans Med Imaging. 2019 Feb 11. doi: 10.1109/TMI.2019.2897943. [Epub ahead of print]

PMID:
30762536
6.

Memory CD4+ T cells are generated in the human fetal intestine.

Li N, van Unen V, Abdelaal T, Guo N, Kasatskaya SA, Ladell K, McLaren JE, Egorov ES, Izraelson M, Chuva de Sousa Lopes SM, Höllt T, Britanova OV, Eggermont J, de Miranda NFCC, Chudakov DM, Price DA, Lelieveldt BPF, Koning F.

Nat Immunol. 2019 Mar;20(3):301-312. doi: 10.1038/s41590-018-0294-9. Epub 2019 Jan 21.

PMID:
30664737
7.

A novel software tool for semi-automatic quantification of thoracic aorta dilatation on baseline and follow-up computed tomography angiography.

Gao X, Boccalini S, Kitslaar PH, Budde RPJ, Tu S, Lelieveldt BPF, Dijkstra J, Reiber JHC.

Int J Cardiovasc Imaging. 2019 Apr;35(4):711-723. doi: 10.1007/s10554-018-1488-9. Epub 2018 Dec 14.

8.

A model-guided method for improving coronary artery tree extractions from CCTA images.

Cao Q, Broersen A, Kitslaar PH, Lelieveldt BPF, Dijkstra J.

Int J Comput Assist Radiol Surg. 2019 Feb;14(2):373-383. doi: 10.1007/s11548-018-1891-7. Epub 2018 Nov 28.

9.

A structural equation model for imaging genetics using spatial transcriptomics.

Huisman SMH, Mahfouz A, Batmanghelich NK, Lelieveldt BPF, Reinders MJT; Alzheimer’s Disease Neuroimaging Initiative.

Brain Inform. 2018 Nov 2;5(2):13. doi: 10.1186/s40708-018-0091-0.

10.

Heterogeneity of circulating CD8 T-cells specific to islet, neo-antigen and virus in patients with type 1 diabetes mellitus.

Laban S, Suwandi JS, van Unen V, Pool J, Wesselius J, Höllt T, Pezzotti N, Vilanova A, Lelieveldt BPF, Roep BO.

PLoS One. 2018 Aug 8;13(8):e0200818. doi: 10.1371/journal.pone.0200818. eCollection 2018.

11.

Histogram-based standardization of intravascular optical coherence tomography images acquired from different imaging systems.

Liu S, Dzyubachyk O, Eggermont J, Nakatani S, Lelieveldt BPF, Dijkstra J.

Med Phys. 2018 Jul 24. doi: 10.1002/mp.13103. [Epub ahead of print]

PMID:
30039851
12.

Integrating spatial-anatomical regularization and structure sparsity into SVM: Improving interpretation of Alzheimer's disease classification.

Sun Z, Qiao Y, Lelieveldt BPF, Staring M; Alzheimer's Disease NeuroImaging Initiative.

Neuroimage. 2018 Sep;178:445-460. doi: 10.1016/j.neuroimage.2018.05.051. Epub 2018 May 23.

13.

Mass cytometry reveals innate lymphoid cell differentiation pathways in the human fetal intestine.

Li N, van Unen V, Höllt T, Thompson A, van Bergen J, Pezzotti N, Eisemann E, Vilanova A, Chuva de Sousa Lopes SM, Lelieveldt BPF, Koning F.

J Exp Med. 2018 May 7;215(5):1383-1396. doi: 10.1084/jem.20171934. Epub 2018 Mar 6.

14.

Author Correction: Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy.

Doorenweerd N, Mahfouz A, van Putten M, Kaliyaperumal R, T' Hoen PAC, Hendriksen JGM, Aartsma-Rus AM, Verschuuren JJGM, Niks EH, Reinders MJT, Kan HE, Lelieveldt BPF.

Sci Rep. 2018 Mar 1;8(1):4058. doi: 10.1038/s41598-018-22154-7.

15.

Interactive Visual Exploration of 3D Mass Spectrometry Imaging Data Using Hierarchical Stochastic Neighbor Embedding Reveals Spatiomolecular Structures at Full Data Resolution.

Abdelmoula WM, Pezzotti N, Hölt T, Dijkstra J, Vilanova A, McDonnell LA, Lelieveldt BPF.

J Proteome Res. 2018 Mar 2;17(3):1054-1064. doi: 10.1021/acs.jproteome.7b00725. Epub 2018 Feb 15.

16.

Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington's Disease.

Keo A, Aziz NA, Dzyubachyk O, van der Grond J, van Roon-Mom WMC, Lelieveldt BPF, Reinders MJT, Mahfouz A.

Front Mol Neurosci. 2017 Nov 30;10:399. doi: 10.3389/fnmol.2017.00399. eCollection 2017.

17.

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types.

van Unen V, Höllt T, Pezzotti N, Li N, Reinders MJT, Eisemann E, Koning F, Vilanova A, Lelieveldt BPF.

Nat Commun. 2017 Nov 23;8(1):1740. doi: 10.1038/s41467-017-01689-9.

18.

An objective comparison of cell-tracking algorithms.

Ulman V, Maška M, Magnusson KEG, Ronneberger O, Haubold C, Harder N, Matula P, Matula P, Svoboda D, Radojevic M, Smal I, Rohr K, Jaldén J, Blau HM, Dzyubachyk O, Lelieveldt B, Xiao P, Li Y, Cho SY, Dufour AC, Olivo-Marin JC, Reyes-Aldasoro CC, Solis-Lemus JA, Bensch R, Brox T, Stegmaier J, Mikut R, Wolf S, Hamprecht FA, Esteves T, Quelhas P, Demirel Ö, Malmström L, Jug F, Tomancak P, Meijering E, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solorzano C.

Nat Methods. 2017 Dec;14(12):1141-1152. doi: 10.1038/nmeth.4473. Epub 2017 Oct 30.

19.

Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy.

Doorenweerd N, Mahfouz A, van Putten M, Kaliyaperumal R, T' Hoen PAC, Hendriksen JGM, Aartsma-Rus AM, Verschuuren JJGM, Niks EH, Reinders MJT, Kan HE, Lelieveldt BPF.

Sci Rep. 2017 Oct 3;7(1):12575. doi: 10.1038/s41598-017-12981-5. Erratum in: Sci Rep. 2018 Mar 1;8(1):4058.

20.

MRI Mouse Brain Data of Ischemic Lesion after Transient Middle Cerebral Artery Occlusion.

Mulder IA, Khmelinskii A, Dzyubachyk O, de Jong S, Wermer MJH, Hoehn M, Lelieveldt BPF, van den Maagdenberg AMJM.

Front Neuroinform. 2017 Sep 6;11:51. doi: 10.3389/fninf.2017.00051. eCollection 2017. No abstract available.

21.

Computer-aided evaluation of inflammatory changes over time on MRI of the spine in patients with suspected axial spondyloarthritis: a feasibility study.

Aizenberg E, van den Berg R, Ez-Zaitouni Z, van der Heijde D, Reijnierse M, Dzyubachyk O, Lelieveldt BPF.

BMC Med Imaging. 2017 Sep 19;17(1):55. doi: 10.1186/s12880-017-0226-4.

22.

Tissue characterization with depth-resolved attenuation coefficient and backscatter term in intravascular optical coherence tomography images.

Liu S, Sotomi Y, Eggermont J, Nakazawa G, Torii S, Ijichi T, Onuma Y, Serruys PW, Lelieveldt BPF, Dijkstra J.

J Biomed Opt. 2017 Sep;22(9):1-16. doi: 10.1117/1.JBO.22.9.096004.

PMID:
28901053
23.

DeepEyes: Progressive Visual Analytics for Designing Deep Neural Networks.

Pezzotti N, Hollt T, Van Gemert J, Lelieveldt BPF, Eisemann E, Vilanova A.

IEEE Trans Vis Comput Graph. 2018 Jan;24(1):98-108. doi: 10.1109/TVCG.2017.2744358. Epub 2017 Aug 29.

PMID:
28866543
24.

CyteGuide: Visual Guidance for Hierarchical Single-Cell Analysis.

Hollt T, Pezzotti N, van Unen V, Koning F, Lelieveldt BPF, Vilanova A.

IEEE Trans Vis Comput Graph. 2018 Jan;24(1):739-748. doi: 10.1109/TVCG.2017.2744318. Epub 2017 Aug 29.

PMID:
28866537
25.

Quantification of aortic annulus in computed tomography angiography: Validation of a fully automatic methodology.

Gao X, Boccalini S, Kitslaar PH, Budde RPJ, Attrach M, Tu S, de Graaf MA, Ondrus T, Penicka M, Scholte AJHA, Lelieveldt BPF, Dijkstra J, Reiber JHC.

Eur J Radiol. 2017 Aug;93:1-8. doi: 10.1016/j.ejrad.2017.04.020. Epub 2017 Apr 26.

PMID:
28668401
26.

Automatic identification of coronary tree anatomy in coronary computed tomography angiography.

Cao Q, Broersen A, de Graaf MA, Kitslaar PH, Yang G, Scholte AJ, Lelieveldt BPF, Reiber JHC, Dijkstra J.

Int J Cardiovasc Imaging. 2017 Nov;33(11):1809-1819. doi: 10.1007/s10554-017-1169-0. Epub 2017 Jun 24.

27.

Automatic quantification of bone marrow edema on MRI of the wrist in patients with early arthritis: A feasibility study.

Aizenberg E, Roex EAH, Nieuwenhuis WP, Mangnus L, van der Helm-van Mil AHM, Reijnierse M, Bloem JL, Lelieveldt BPF, Stoel BC.

Magn Reson Med. 2018 Feb;79(2):1127-1134. doi: 10.1002/mrm.26712. Epub 2017 May 7. Erratum in: Magn Reson Med. 2019 Jul;82(1):510.

28.

Fully-automatic left ventricular segmentation from long-axis cardiac cine MR scans.

Shahzad R, Tao Q, Dzyubachyk O, Staring M, Lelieveldt BPF, van der Geest RJ.

Med Image Anal. 2017 Jul;39:44-55. doi: 10.1016/j.media.2017.04.004. Epub 2017 Apr 13.

PMID:
28432954
29.

Validation of full-field optical coherence tomography in distinguishing malignant and benign tissue in resected pancreatic cancer specimens.

van Manen L, Stegehuis PL, Fariña-Sarasqueta A, de Haan LM, Eggermont J, Bonsing BA, Morreau H, Lelieveldt BPF, van de Velde CJH, Vahrmeijer AL, Dijkstra J, Mieog JSD.

PLoS One. 2017 Apr 17;12(4):e0175862. doi: 10.1371/journal.pone.0175862. eCollection 2017.

30.

Detection of Conversion from Mild Cognitive Impairment to Alzheimer's Disease Using Longitudinal Brain MRI.

Sun Z, van de Giessen M, Lelieveldt BP, Staring M.

Front Neuroinform. 2017 Feb 24;11:16. doi: 10.3389/fninf.2017.00016. eCollection 2017.

31.

Automated Ischemic Lesion Segmentation in MRI Mouse Brain Data after Transient Middle Cerebral Artery Occlusion.

Mulder IA, Khmelinskii A, Dzyubachyk O, de Jong S, Rieff N, Wermer MJ, Hoehn M, Lelieveldt BP, van den Maagdenberg AM.

Front Neuroinform. 2017 Jan 31;11:3. doi: 10.3389/fninf.2017.00003. eCollection 2017.

32.

Toward optical guidance during endoscopic ultrasound-guided fine needle aspirations of pancreatic masses using single fiber reflectance spectroscopy: a feasibility study.

Stegehuis PL, Boogerd LS, Inderson A, Veenendaal RA, van Gerven P, Bonsing BA, Sven Mieog J, Amelink A, Veselic M, Morreau H, van de Velde CJ, Lelieveldt BP, Dijkstra J, Robinson DJ, Vahrmeijer AL.

J Biomed Opt. 2017 Feb 1;22(2):24001. doi: 10.1117/1.JBO.22.2.024001.

PMID:
28170030
33.

BrainScope: interactive visual exploration of the spatial and temporal human brain transcriptome.

Huisman SMH, van Lew B, Mahfouz A, Pezzotti N, Höllt T, Michielsen L, Vilanova A, Reinders MJT, Lelieveldt BPF.

Nucleic Acids Res. 2017 Jun 2;45(10):e83. doi: 10.1093/nar/gkx046.

34.

Approximated and User Steerable tSNE for Progressive Visual Analytics.

Pezzotti N, Lelieveldt BPF, Van Der Maaten L, Hollt T, Eisemann E, Vilanova A.

IEEE Trans Vis Comput Graph. 2017 Jul;23(7):1739-1752. doi: 10.1109/TVCG.2016.2570755. Epub 2016 May 19.

PMID:
28113434
35.

Analysis and compensation for the effect of the catheter position on image intensities in intravascular optical coherence tomography.

Liu S, Eggermont J, Wolterbeek R, Broersen A, Busk CA, Precht H, Lelieveldt BP, Dijkstra J.

J Biomed Opt. 2016 Dec 1;21(12):126005. doi: 10.1117/1.JBO.21.12.126005.

PMID:
27926746
36.

Brain transcriptome atlases: a computational perspective.

Mahfouz A, Huisman SMH, Lelieveldt BPF, Reinders MJT.

Brain Struct Funct. 2017 May;222(4):1557-1580. doi: 10.1007/s00429-016-1338-2. Epub 2016 Dec 1. Review.

37.

EpCAM as multi-tumour target for near-infrared fluorescence guided surgery.

van Driel PB, Boonstra MC, Prevoo HA, van de Giessen M, Snoeks TJ, Tummers QR, Keereweer S, Cordfunke RA, Fish A, van Eendenburg JD, Lelieveldt BP, Dijkstra J, van de Velde CJ, Kuppen PJ, Vahrmeijer AL, Löwik CW, Sier CF.

BMC Cancer. 2016 Nov 14;16(1):884.

38.

Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data.

Abdelmoula WM, Balluff B, Englert S, Dijkstra J, Reinders MJ, Walch A, McDonnell LA, Lelieveldt BP.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12244-12249. Epub 2016 Oct 10.

39.

Noninvasive Detection of Metastases and Follicle Density in Ovarian Tissue Using Full-Field Optical Coherence Tomography.

Peters IT, Stegehuis PL, Peek R, Boer FL, van Zwet EW, Eggermont J, Westphal JR, Kuppen PJ, Trimbos JB, Hilders CG, Lelieveldt BP, van de Velde CJ, Bosse T, Dijkstra J, Vahrmeijer AL.

Clin Cancer Res. 2016 Nov 15;22(22):5506-5513. doi: 10.1158/1078-0432.CCR-16-0288. Epub 2016 May 16.

40.

Mass Cytometry of the Human Mucosal Immune System Identifies Tissue- and Disease-Associated Immune Subsets.

van Unen V, Li N, Molendijk I, Temurhan M, Höllt T, van der Meulen-de Jong AE, Verspaget HW, Mearin ML, Mulder CJ, van Bergen J, Lelieveldt BP, Koning F.

Immunity. 2016 May 17;44(5):1227-39. doi: 10.1016/j.immuni.2016.04.014. Epub 2016 May 10.

41.

Assessment of viscous energy loss and the association with three-dimensional vortex ring formation in left ventricular inflow: In vivo evaluation using four-dimensional flow MRI.

Elbaz MS, van der Geest RJ, Calkoen EE, de Roos A, Lelieveldt BP, Roest AA, Westenberg JJ.

Magn Reson Med. 2017 Feb;77(2):794-805. doi: 10.1002/mrm.26129. Epub 2016 Feb 28.

42.

Gene co-expression analysis identifies brain regions and cell types involved in migraine pathophysiology: a GWAS-based study using the Allen Human Brain Atlas.

Eising E, Huisman SMH, Mahfouz A, Vijfhuizen LS, Anttila V, Winsvold BS, Kurth T, Ikram MA, Freilinger T, Kaprio J, Boomsma DI, van Duijn CM, Järvelin MR, Zwart JA, Quaye L, Strachan DP, Kubisch C, Dichgans M, Davey Smith G, Stefansson K, Palotie A, Chasman DI, Ferrari MD, Terwindt GM, de Vries B, Nyholt DR, Lelieveldt BPF, van den Maagdenberg AMJM, Reinders MJT.

Hum Genet. 2016 Apr;135(4):425-439. doi: 10.1007/s00439-016-1638-x. Epub 2016 Feb 22.

43.

Inter-station intensity standardization for whole-body MR data.

Dzyubachyk O, Staring M, Reijnierse M, Lelieveldt BP, van der Geest RJ.

Magn Reson Med. 2017 Jan;77(1):422-433. doi: 10.1002/mrm.26098. Epub 2016 Feb 1.

44.

Genome-wide coexpression of steroid receptors in the mouse brain: Identifying signaling pathways and functionally coordinated regions.

Mahfouz A, Lelieveldt BP, Grefhorst A, van Weert LT, Mol IM, Sips HC, van den Heuvel JK, Datson NA, Visser JA, Reinders MJ, Meijer OC.

Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):2738-43. doi: 10.1073/pnas.1520376113. Epub 2016 Jan 25.

45.

Morphological maturation of the mouse brain: An in vivo MRI and histology investigation.

Hammelrath L, Škokić S, Khmelinskii A, Hess A, van der Knaap N, Staring M, Lelieveldt BPF, Wiedermann D, Hoehn M.

Neuroimage. 2016 Jan 15;125:144-152. doi: 10.1016/j.neuroimage.2015.10.009. Epub 2015 Oct 14.

46.

Shared Pathways Among Autism Candidate Genes Determined by Co-expression Network Analysis of the Developing Human Brain Transcriptome.

Mahfouz A, Ziats MN, Rennert OM, Lelieveldt BP, Reinders MJ.

J Mol Neurosci. 2015 Dec;57(4):580-94. doi: 10.1007/s12031-015-0641-3. Epub 2015 Sep 23.

47.

Fast Automatic Step Size Estimation for Gradient Descent Optimization of Image Registration.

Qiao Y, van Lew B, Lelieveldt BP, Staring M.

IEEE Trans Med Imaging. 2016 Feb;35(2):391-403. doi: 10.1109/TMI.2015.2476354. Epub 2015 Sep 3.

PMID:
26353367
48.

Repeatability of in vivo quantification of atherosclerotic carotid artery plaque components by supervised multispectral classification.

Gao S, van 't Klooster R, van Wijk DF, Nederveen AJ, Lelieveldt BP, van der Geest RJ.

MAGMA. 2015 Dec;28(6):535-45. doi: 10.1007/s10334-015-0495-2. Epub 2015 Jul 11.

49.

Automated extraction and labelling of the arterial tree from whole-body MRA data.

Shahzad R, Dzyubachyk O, Staring M, Kullberg J, Johansson L, Ahlström H, Lelieveldt BPF, van der Geest RJ.

Med Image Anal. 2015 Aug;24(1):28-40. doi: 10.1016/j.media.2015.05.008. Epub 2015 May 21.

PMID:
26057864
50.

Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.

Babaei S, Mahfouz A, Hulsman M, Lelieveldt BP, de Ridder J, Reinders M.

PLoS Comput Biol. 2015 May 12;11(5):e1004221. doi: 10.1371/journal.pcbi.1004221. eCollection 2015 May.

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