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CIRRUS Lung

CIRRUS Lung is a workstation for quantitative analysis of thoracic CT scans. It includes a wide variety of algorithms that have been developed and collected over a period of a decade. This page provides an overview of features and a list of publications that have used CIRRUS Lung or its underlying technology, and describe the technical details of the algorithms.

Features

Segmentation of pulmonary anatomy

Registration

  • Registration of temporal scans
  • Registration of inspiration - expiration scans
  • Linked scrolling

Nodule analysis

  • Computer-aided detection of solid nodules
  • Computer-aided detection of non-solid and part-solid nodules
  • Volumetry of solid, non-solid, and part-solid nodules using automatic presets and minimal user interaction
  • Computation of volume, mass, growth rate and doubling time

Emphysema and airway analysis

  • Emphysema quantifications using density mask and percentile scores per lung, lobe, and segment
  • Core and rind measurements
  • Cluster size measurements
  • Airway wall analysis
  • Trachea shape analysis
  • Quantifications of airtrapping using density mask per lung, lobe, and segment
  • Joint histogram analysis of inspiratory and expiratory scans (PRM maps)

COPD applications

  • Fissural integrity measurements
  • Normalization of emphysema quantifications obtained from scans acquired with different reconstruction parameters

Clinical publications that have used CIRRUS Lung

F.A.A. Mohamed Hoesein, M. Schmidt, O.M. Mets, H.A. Gietema, J.-W.J. Lammers, P. Zanen, H.J. de Koning, C. van der Aalst, M. Oudkerk, R. Vliegenthart, I. Isgum, M. Prokop, B. van Ginneken, E.M. van Rikxoort and P.A. de Jong. "Discriminating dominant computed tomography phenotypes in smokers without or with mild COPD",Respiratory Medicine. Abstract DOI PMID

E.T. Scholten, C. Jacobs, B. van Ginneken, M.J. Willemink, J.-M. Kuhnigk, P.M.A. van Ooijen, M. Oudkerk, W.P.T.M. Mali and P.A. de Jong. "Computer-Aided Segmentation and Volumetry of Artificial Ground-Glass Nodules at Chest CT", American Journal of Roentgenology 2013;201:295-300. Abstract/PDF DOI PMID

E.M. van Rikxoort and B. van Ginneken. "Automated segmentation of pulmonary structures in thoracic computed tomography scans: a review", Physics in Medicine and Biology 2013;58:R187-R220. Abstract/PDF DOI PMID

O.M. Mets, M. Schmidt, C.F. Buckens, M.J. Gondrie, I. Isgum, M. Oudkerk, R. Vliegenthart, H.J. de Koning, C.M. van der Aalst, M. Prokop, J.-W.J. Lammers, P. Zanen, F.A. Mohamed Hoesein, W.P. Mali, B. van Ginneken, E.M. van Rikxoort and P.A. de Jong. "Diagnosis of chronic obstructive pulmonary disease in lung cancer screening Computed Tomography scans: independent contribution of emphysema, air trapping and bronchial wall thickening.",Respiratory Research 2013;14(1):59. Abstract/PDF DOI PMID

F. A. Mohamed Hoesein, P.A. de Jong, J.-W.J. Lammers, W.P. Mali, M. Schmidt, H.J. de Koning, C. van der Aalst, M. Oudkerk, R. Vliegenthart, B. van Ginneken, E.M. van Rikxoort and P. Zanen. "Computed tomography structural lung changes in discordant airflow obstruction", PLoS One 2013;8(6):e65177. Abstract/PDF DOI

F.A. Mohamed Hoesein, P. Zanen, P.A. de Jong, B. van Ginneken, H.M. Boezen, H.J. Groen, M. Oudkerk, H.J. de Koning, D.S. Postma and J.-W.J. Lammers. "Rate of progression of CT-quantified emphysema in male current and ex-smokers: a follow-up study", Respiratory Research 2013;14:55. Abstract/PDF DOI PMID

O.M. Mets, P.A. de Jong, B. van Ginneken, C.L.J.J. Kruitwagen, M. Prokop, M. Oudkerk, J.-W.J. Lammers and P. Zanen. "CT Air Trapping Is Independently Associated with Lung Function Reduction over Time", PLoS One2013;8:e61783. Abstract/PDF DOI PMID

N. Fens, A.G.J. van Rossum, P. Zanen, B. van Ginneken, R.J. van Klaveren, A.H. Zwinderman and P.J. Sterk. "Subphenotypes of Mild-to-Moderate COPD by Factor and Cluster Analysis of Pulmonary Function, CT Imaging and Breathomics in a Population-Based Survey", COPD 2013;10:277-285. Abstract DOI PMID

A.E. Dijkstra, D.S. Postma, N. Ten Hacken, J.M. Vonk, M. Oudkerk, P.M. van Ooijen, P. Zanen, F.A. Mohamed Hoesein, B. van Ginneken, M. Schmidt and H.J. Groen. "Low-dose CT measurements of airway dimensions and emphysema associated with airflow limitation in heavy smokers: a cross sectional study", *Respiratory Research *2013;14:11. Abstract DOI PMID

O.M. Mets, P. Zanen, J.-W.J. Lammers, I. Isgum, H.A. Gietema, B. van Ginneken, M. Prokop and P.A. de Jong. "Early Identification of Small Airways Disease on Lung Cancer Screening CT: Comparison of Current Air Trapping Measures", Lung 2012;190:629-633. Abstract/PDF DOI PMID

O.M. Mets, R.A. van Hulst, C. Jacobs, B. van Ginneken and P.A. de Jong. "Normal Range of Emphysema and Air Trapping on CT in Young Men", American Journal of Roentgenology 2012;199:336-340. Abstract/PDF DOI PMID

F.A.A.M. Hoesein, P. Zanen, H.M. Boezen, H.J.M. Groen, B. van Ginneken, P.A. de Jong, D.S. Postma and J.-W.J. Lammers. "Lung function decline in heavy male smokers relates to baseline airflow obstruction severity", Chest2012;142:1530-1538. Abstract/PDF DOI PMID Google Scholar

F.A.A.M. Hoesein, E.M. van Rikxoort, B. van Ginneken, P.A. de Jong, M. Prokop, J.-W.J. Lammers and P. Zanen. "CT-quantified emphysema distribution is associated with lung function decline", European Respiratory Journal2012;40:844-850. Abstract/PDF DOI PMID Google Scholar

O.M. Mets, K. Murphy, P. Zanen, H.A. Gietema, J.W. Lammers, B. van Ginneken, M. Prokop and P.A. de Jong. "The relationship between lung function impairment and quantitative computed tomography in chronic obstructive pulmonary disease", European Radiology 2012;22:120-128. Abstract/PDF DOI PMID Google Scholar

E.M. van Rikxoort, J. Goldin, F. Abtin, H.J. Kim, P. Lu, B. van Ginneken, G. Shaw, M. Galperin-Aizenberg and M.S. Brown. "A method for the automatic quantification of the completeness of pulmonary fissures: evaluation in a database of subjects with severe emphysema", European Radiology 2012;22:302-309. Abstract/PDF DOI PMID Google Scholar

O.M. Mets, C.F.M. Buckens, P. Zanen, I. Isgum, B. van Ginneken, M. Prokop, H.A. Gietema, J.W.J. Lammers, R. Vliegenthart, M. Oudkerk, R.J. van Klaveren, H.J. de Koning, W.P.T.M. Mali and P.A. de Jong. "Identification of Chronic Obstructive Pulmonary Disease in Lung Cancer Screening Computed Tomographic Scans", Journal of the American Medical Association 2011;306:1775-1781. Abstract/PDF DOI PMID Google Scholar

F.A.A.M. Hoesein, P. Zanen, B. van Ginneken, R.J. van Klaveren and J.-W.J. Lammers. "Association of the transfer coefficient of the lung for carbon monoxide with emphysema progression in male smokers", European Respiratory Journal 2011;38:1012-1018. Abstract/PDF DOI PMID Google Scholar

F.A.A.M. Hoesein, B. de Hoop, P. Zanen, H. Gietema, C.L.J.J. Kruitwagen, B. van Ginneken, I. Isgum, C. Mol, R.J. van Klaveren, A.E. Dijkstra, H.J.M. Groen, H.M. Boezen, D.S. Postma, M. Prokop and J.-W.J. Lammers. "CT-quantified emphysema in male heavy smokers: association with lung function decline", Thorax 2011;66:782-787.Abstract/PDF DOI PMID Google Scholar

H.A. Gietema, P. Zanen, A. Schilham, B. van Ginneken, R.J. van Klaveren, M. Prokop and J.W. Lammers. "Distribution of emphysema in heavy smokers: impact on pulmonary function", Respiratory Medicine2010;104:76-82. Abstract/PDF DOI PMID Google Scholar

X. Artaechevarria, D. Pérez-Martin, M. Ceresa, G. de Biurrun, D. Blanco, L.M. Montuenga, B. van Ginneken, C.O. de Solórzano and A. Muñoz-Barrutia. "Airway segmentation and analysis for the study of mouse models of lung disease using micro-CT", Physics in Medicine and Biology 2009;54:7009-7024. Abstract/PDF DOI PMID Google Scholar

B. de Hoop, H. Gietema, B. van Ginneken, P. Zanen, G. Groenewegen and M. Prokop. "A comparison of six software packages for evaluation of solid lung nodules using semi-automated volumetry: what is the minimum increase in size to detect growth in repeated CT examinations", European Radiology 2009;19:800-808.Abstract/PDF DOI PMID Google Scholar

M. Staring, J.P.W. Pluim, B.J. de Hoop, S. Klein, B. van Ginneken, H. Gietema, G. Nossent, C.M. Schaefer-Prokop, S. van de Vorst and M. Prokop. "Image Subtraction Facilitates Assessment of Volume and Density Change in Ground-Glass Opacities in Chest CT", Investigative Radiology 2009;44:61-66. Abstract/PDF DOI PMID Google Scholar

H.A. Gietema, A.M. Schilham, B. van Ginneken, R.J. van Klaveren, J.W.J. Lammers and M. Prokop. "Monitoring of smoking-induced emphysema with CT in a lung cancer screening setting: detection of real increase in extent of emphysema", Radiology 2007;244:890-897. Abstract/PDF DOI PMID Google Scholar

Technical publications about algorithms included in CIRRUS Lung

B. Lassen, E.M. van Rikxoort, M. Schmidt, S. Kerkstra, B. van Ginneken and J. Kuhnigk. "Automatic segmentation of the pulmonary lobes from chest CT scans based on fissures, vessels, and bronchi", IEEE Transactions on Medical Imaging 2013;32:210-222. Abstract/PDF DOI PMID Google Scholar

L. Gallardo-Estrella, B. van Ginneken and E.M. van Rikxoort. "Normalization of CT scans reconstructed with different kernels to reduce variability in emphysema measurements", in: Medical Imaging, volume 8670 of Proceedings of the SPIE, 2013, page 86700E. Abstract/PDF DOI

P. Lo, B. van Ginneken, J.M. Reinhardt, Y. Tarunashree, P.A. de Jong, B. Irving, C. Fetita, M. Ortner, R. Pinho, J. Sijbers, M. Feuerstein, A. Fabijanska, C. Bauer, R. Beichel, C.S. Mendoza, R. Wiemker, J. Lee, A.P. Reeves, S. Born, O. Weinheimer, E.M. van Rikxoort, J. Tschirren, K. Mori, B. Odry, D.P. Naidich, I.J. Hartmann, E.A. Hoffman, M. Prokop, J.H. Pedersen and M. de Bruijne. "Extraction of Airways from CT (EXACT'09)", IEEE Transactions on Medical Imaging 2012;31:2093-2107. Abstract/PDF DOI PMID Google Scholar

K. Murphy, J.P.W. Pluim, E.M. van Rikxoort, P.A. de Jong, B. de Hoop, H.A. Gietema, O. Mets, M. de Bruijne, P. Lo, M. Prokop and B. van Ginneken. "Toward automatic regional analysis of pulmonary function using inspiration and expiration thoracic CT", Medical Physics 2012;39:1650-1662. Abstract/PDF DOI PMID

E.M. van Rikxoort, P.A. de Jong, O.M. Mets and B. van Ginneken. "Automatic classication of pulmonary function in COPD patients using trachea analysis in chest CT scans", in: Medical Imaging, volume 8315 of Proceedings of the SPIE, 2012, pages 83150P-83150P-6. Abstract/PDF DOI

K. Murphy, B. van Ginneken, J.M. Reinhardt, S. Kabus, K. Ding, X. Deng, K. Cao, K. Du, G.E. Christensen, V. Garcia, T. Vercauteren, N. Ayache, O. Commowick, G. Malandain, B. Glocker, N. Paragios, N. Navab, V. Gorbunova, J. Sporring, M. de Bruijne, X. Han, M.P. Heinrich, J.A. Schnabel, M. Jenkinson, C. Lorenz, M. Modat, J.R. McClelland, S. Ourselin, S.E.A. Muenzing, M.A. Viergever, D.D. Nigris, D.L. Collins, T. Arbel, M. Peroni, R. Li, G.C. Sharp, A. Schmidt-Richberg, J. Ehrhardt, R. Werner, D. Smeets, D. Loeckx, G. Song, N. Tustison, B. Avants, J.C. Gee, M. Staring, S. Klein, B.C. Stoel, M. Urschler, M. Werlberger, J. Vandemeulebroucke, S. Rit, D. Sarrut and J.P.W. Pluim. "Evaluation of Registration Methods on Thoracic CT: The EMPIRE10 Challenge", IEEE Transactions on Medical Imaging 2011;31:1901-1920. Abstract/PDF DOI PMID Google Scholar

M. Niemeijer, M. Loog, M.D. Abràmoff, M.A. Viergever, M. Prokop and B. van Ginneken. "On Combining Computer-Aided Detection Systems", IEEE Transactions on Medical Imaging 2011;30:215-223. Abstract/PDF DOI PMID Google Scholar

C. Jacobs, K. Murphy, T. Twellmann, P.A. de Jong and B. van Ginneken. "Computer-Aided Detection of Solid and Ground Glass Nodules in Thoracic CT images using two independent CAD systems", in: The Fourth International Workshop on Pulmonary Image Analysis, 2011. Abstract/PDF

E.M. van Rikxoort and B. van Ginneken. "Automatic segmentation of the lungs and lobes from thoracic CT scans", in: The Fourth International Workshop on Pulmonary Image Analysis, 2011, pages 261-268. Abstract

C. Jacobs, C.I. Sánchez, S.C. Saur, T. Twellmann, P.A. de Jong and B. van Ginneken. "Computer-Aided Detection of Ground Glass Nodules in Thoracic CT images using Shape, Intensity and Context Features", in: Medical Image Computing and Computer-Assisted Intervention, volume 6893 of Lecture Notes in Computer Science, 2011, pages 207-214. Abstract/PDF DOI PMID Google Scholar

B. van Ginneken, S.G. Armato, B. de Hoop, S. van de Vorst, T. Duindam, M. Niemeijer, K. Murphy, A.M.R. Schilham, A. Retico, M.E. Fantacci, N. Camarlinghi, F. Bagagli, I. Gori, T. Hara, H. Fujita, G. Gargano, R. Belloti, F.D. Carlo, R. Megna, S. Tangaro, L. Bolanos, P. Cerello, S.C. Cheran, E.L. Torres and M. Prokop. "Comparing and combining algorithms for computer-aided detection of pulmonary nodules in computed tomography scans: the ANODE09 study", Medical Image Analysis 2010;14:707-722. Abstract/PDF DOI PMID Google Scholar

E.M. van Rikxoort, M. Prokop, B. de Hoop, M. Viergever, J. Pluim and B. van Ginneken. "Automatic Segmentation of Pulmonary Lobes Robust Against Incomplete Fissures", IEEE Transactions on Medical Imaging 2010;29:1286-1296. Abstract/PDF DOI PMID Google Scholar

Y. Arzhaeva, M. Prokop, K. Murphy, E.M. van Rikxoort, P.A. de Jong, H.A. Gietema, M.A. Viergever and B. van Ginneken. "Automated estimation of progression of interstitial lung disease in CT images", Medical Physics2010;37:63-73. Abstract/PDF DOI PMID Google Scholar

E. van Dongen and B. van Ginneken. "Automatic segmentation of pulmonary vasculature in thoracic CT scans with local thresholding and airway wall removal", in: IEEE International Symposium on Biomedical Imaging, 2010, pages 668-671. Abstract/PDF DOI

E.M. van Rikxoort, B. de Hoop, M.A. Viergever, M. Prokop and B. van Ginneken. "Automatic lung segmentation from thoracic computed tomography scans using a hybrid approach with error detection", *Medical Physics *2009;36:2934-2947. Abstract/PDF DOI PMID Google Scholar

K. Murphy, B. van Ginneken, A.M.R. Schilham, B.J. de Hoop, H.A. Gietema and M. Prokop. "A Large Scale Evaluation of Automatic Pulmonary Nodule Detection in Chest CT using Local Image Features and k-Nearest-Neighbour Classification", Medical Image Analysis 2009;13:757-770. Abstract/PDF DOI PMID Google Scholar

E.M. van Rikxoort, B. de Hoop, S. van de Vorst, M. Prokop and B. van Ginneken. "Automatic segmentation of pulmonary segments from volumetric chest CT scans", IEEE Transactions on Medical Imaging 2009;28:621-630.Abstract/PDF DOI PMID Google Scholar

E.M. van Rikxoort, M. Prokop, B. de Hoop, M.A. Viergever, J.P.W. Pluim and B. van Ginneken. "Automatic segmentation of the pulmonary lobes from fissures, airways, and lung borders: evaluation of robustness against missing data", in: Medical Image Computing and Computer-Assisted Intervention of Lecture Notes in Computer Science, 2009, pages 263-271. Abstract/PDF DOI PMID Google Scholar

E.M. van Rikxoort, B. van Ginneken, M. Klik and M. Prokop. "Supervised enhancement filters: application to fissure detection in chest CT scans", IEEE Transactions on Medical Imaging 2008;27:1-10. Abstract/PDF DOI PMID Google Scholar

E.M. van Rikxoort, M. de Bruijne and B. van Ginneken. "Integrating local voxel classification and global shape models for medical image segmentation", in: Medical Imaging of Proceedings of the SPIE, 2008, pages 69144J-1 - 69144J-6. PDF DOI

B. van Ginneken, A. Tan, K. Murphy, B.J. de Hoop and M. Prokop. "Automated detection of nodules attached to the pleural and mediastinal surface in low-dose CT scans", in: Medical Imaging, volume 6915 of Proceedings of the SPIE, 2008, pages 69150X1-69150X10. Abstract/PDF DOI

B. van Ginneken, W. Baggerman and E.M. van Rikxoort. "Robust segmentation and anatomical labeling of the airway tree from thoracic CT scans", in: Medical Image Computing and Computer-Assisted Intervention, volume 5241 of Lecture Notes in Computer Science, 2008, pages 219-226. Abstract/PDF DOI PMID Google Scholar

I.C. Sluimer, M. Prokop, I. Hartmann and B. van Ginneken. "Automated classification of hyperlucency, fibrosis, ground glass, solid and focal lesions in high resolution CT of the lung", Medical Physics 2006;33:2610-2620.Abstract/PDF DOI PMID Google Scholar

A.M.R. Schilham, B. van Ginneken, H. Gietema and M. Prokop. "Local noise weighted filtering for emphysema scoring of low-dose CT images", IEEE Transactions on Medical Imaging 2006;25:451-463. Abstract/PDF DOI PMID Google Scholar

M.A.J. Klik, E.M. van Rikxoort, J.F. Peters, H.A. Gietema, M. Prokop and B. van Ginneken. "Improved classification of pulmonary nodules by automated detection of benign subpleural lymph nodes", in: IEEE International Symposium on Biomedical Imaging, 2006, pages 494-497. Abstract/PDF DOI Google Scholar

I. Sluimer, M. Prokop and B. van Ginneken. "Towards automated segmentation of the pathological lung in CT",IEEE Transactions on Medical Imaging 2005;24:1025-1038. Abstract/PDF DOI PMID Google Scholar

I.C. Sluimer, P.F. van Waes, M.A. Viergever and B. van Ginneken. "Computer-aided diagnosis in high-resolution CT of the lungs", Medical Physics 2003;30:3081-3090. Abstract/PDF DOI PMID Google Scholar