Dr. M. Els Bakker

Senior researcher


  • Pulmonary image processing
  • Validation of developed pulmonary sofware
  • Financial project management
  • Works council


M. Els Bakker studied Biology at the University of Leiden. She graduated in August 1983. From 1987-1991 she worked as PhD student at National Herbarium in Leiden and successfully defended her thesis in November 1992. From 1996-2000 she worked at the Expert Centre of Taxonomy in Amsterdam collecting data for 2 botanical cd-roms. Further she digitized part of the microscopical wood collection at the Herbarium of Utrecht.

In February 2001 she joined the Division of Image Processing at the Leiden University Medical Center, as the coordinator of the 5th frame project SPREAD (Software Performance and Reproducibility in Emphysema Assessment: Demonstration). The task also included the validation of the developed software for assessing emphysema severity (Pulmo-CMS).

Since 2005 she is working as a post-doctoral researcher and validates the software that is being developed within the research group in the area of lung emphysema, the bronchial tree and the vascular tree in the lungs.

Furthermore, she is responsible for the financial management of the research projects running within LKEB.


  • Ninaber MK, Stolk J, Smit J. Le Roy EJ, Kroft LJM, Bakker ME, de Vries Bouwstra JK, Schouffoer AA, Staring M, Stoel BC. Lung structure and function relation in systemic sclerosis: Application of lung densitometry. European Journal of Radiology 01/2015; 84(5):975-979.
  • Staring M, Bakker ME, Stolk J, Shamonin DP, Reiber JHC, Stoel BC. Towards local progression estimation of pulmonary emphysema using CT. Medical Physics 02/2014; 41(2):021905.
  • Shamonin DP, Staring M, Bakker ME, Xiao C, Stolk J, Reiber JHC, Stoel BC. Automatic lung lobe segmentation of COPD patients using iterative B-spline fitting. Proceedings of SPIE - The International Society for Optical Engineering 02.2012; DOI: 10.1117/12.910869. 
  • Agarwal M, Hendriks EA, Stoel BC, Bakker ME, Reiber JHC, Staring M. Local SIMPLE multi-atlas-based segmentation applied to lung lobe detection on chest CT/ Proceedings of SPIE - The International Society for Optical Engineering 02/2012; DOI: 10.1117/12.911552.
  • Bakker ME, Stolk J, Reiber JHC, Stoel BC. Influence of inspiration level on bronchial lumen measurements with computed tomography. Repiratory Medicine 2012; 106:677-686.
  • Stoel BC, Dirksen A, Stockley RA, Parr D, Piitulainen E, Shaker SB, Russi EW, Bakker ME, Reiber JHC, Stolk J. Eureka? Radiology 05/2011; 259(2):610-611
  • Stoel BC, Bakker E, Reiber H, Stolk J. Confounding factors in gender-related differences in emphysema detected by CT densitometry. American Thoracic Society 2010 International Conference, May 14-19, 2010 New Orleans; 05/2010 (conference paper).
  • Fregonese L, Llado Puidgemont A, Bakker EM, Stoel BC, Stolk J. The contribution of teh nitrogen washout test to phenotyping in alpha-1-antitrypsin deficient emphysema. American Thoracic Society 2009 International Conference, May 15-20, 2009 San Diego, California; 04/2009 (conference paper).
  • Staring M, Bakker ME, Shamonin DP, Stolk J, Reiber JHC, Stoel BC. Towards local estimation of emphysema progression using image registration. Proceedings of SPIE - The International Society for Optical Engineering 02/2009; DOI:10.1117/12.811576.
  • Stoel BC, Parr DG, Bakker EM, Putter H, Stolk J, Gietema HA, Schilham AM, van Ginneken B, van Klaveren RJ, Lammer WJ, Prokop M. Can the extent of low-attenuation areas on CT scans really demonstrate changes in teh severity of emhysema? Radiology 05/2008; 247(1):293-294; author reply 294. DIO:10.1148/radiol.2471071608.
  • Stoel BC, Putter H, Bakker ME, Dirksen A, Stockley RA, Piitulainen E, Russi EW, Parr D, Shaker SB, Reiber JH, Stolk J. Volume correction in computed tomography densitometry for follow-up studies on pulmonary emphysema. Proc Am Thorac Soc. 2008 Dec 15;5(9):919-24
  • Bakker ME, Putter H, Stolk J, Shaker SB, Piitulainen E, Russi EW, Stoel BC. Assessment of regional progression of pulmonary emphysema with CT densitometry. Chest. 2008 Nov;134(5):931-7.
  • Stolk J, Versteegh MI, Montenij LJ, Bakker ME, Grebski E, Tutic M, Wildermuth S, Weder W, el Bardiji M, Reiber JH, Rabe KF, Russi EW, Stoel BC. Densitometry for assessment of effect of lung volume reduction surgery for emphysema. Eur Respir J. 2007 Jun;29(6):1138-43.
  • Bakker ME, Stolk J, Putter H, Shaker SB, Parr DG, Piitulainen E, Russi EW, Dirksen A, Stockley RA, Reiber JH, Stoel BC. Variability in densitometric assessment of pulmonary emphysema with computed tomography. Invest Radiol. 2005 Dec;40(12):777-83.
  • Stoel BC, Bakker ME, Stolk J, Dirksen A, Stockley RA, Piitulainen E, Russi EW, Reiber JH. Comparison of the sensitivities of 5 different computed tomography scanners for the assessment of the progression of pulmonary emphysema: a phantom study. Invest Radiol. 2004 Jan;39(1):1-7.
  • Stolk J, Ng WH, Bakker ME, Reiber JH, Rabe KF, Putter H, Stoel BC. Correlation between annual change in health status and computer tomography derived lung density in subjects with alpha1-antitrypsin deficiency. Thorax. 2003 Dec;58(12):1027-30.


Leids Universitair Medisch Centrum
Gebouw 1
Kamer C3-52

Albinusdreef 2
2333 ZA Leiden
Tel: +31 (0) 71 526 1246

Postzone C2-S
Postbus 9600
2300 RC Leiden

E-mail: M.E.Bakker@lumc.nl