National Institute of Standards and Technology

Publications

Data and Software Dissemination

Data dissemination: Image Segmentation

Survey Statistics of Automated Segmentations Applied to Optical Imaging of Mammalian Cells (pdf): Peter Bajcsy, Antonio Cardone, Joe Chalfoun, Michael Halter, Derek Juba, Marcin Kociolek, Michael Majurski, Adele Peskin, Carl Simon, Mylene Simon, Antoine Vandecreme, and Mary Brady
BMC Bioinformatics, 2015, 16:330. doi: 10.1186/s12859-015-0762-2
Comparison of segmentation algorithms for fluorescence microscopy images of cells. (pdf): Dima, Alden, John Elliott, James Filliben, Michael Halter, Adele Peskin, Javier Bernal, Marcin Kociolek, Mary Brady, Hai Tang, Anne Plant.
Cytometry Part A, 79A: 545-559, 2011

Software dissemination: Software For Microscopy Image Analyses

Web Microanalysis of Big Image Data: Peter Bajcsy, Joe Chalfoun, and Mylene Simon
Book, Publisher: Springer-Verlag International, February 2018
A Map App to Track Stem Cells. (src): Alison Gillespie.
SPIE (International Society for Optics and Photonics ) News about Biomedical Optics & Medical Imaging, March 16th, 2018.

Cell Biology Applications

2D + spectral Measurement of Tissues

Accurate and Interpretable Classification of Microspectroscopy Pixels Using Artificial Neural Networks: Petre Manescu, Young Lee, Charles Camp, Marc Cicerone, Mary Brady, and Peter Bajcsy
Elsevier Medical Image Analysis, Volume 37, April 2017, Pages 37–45; DOI: https://dx.doi.org/10.1016/j.media.2017.01.001

2D + time Measurement of Stem Cells Pluripotency

MIST Accurate and Scalable Microscopy Image Stitching Method with Stage Modeling and Error Minimization: Joe Chalfoun, Michael Majurski, Tim Blattner, Walid Keyrouz, Peter Bajcsy, and Mary Brady
Nature Scientific Reports, July 2017; DOI: 10.1038/s41598-017-04567-y (SREP-17-02878)
Do We Trust Image Measurements? Variability, Accuracy and Traceability of Image Features (pdf): Mylene Simon, Joe Chalfoun, Mary Brady, and Peter Bajcsy
IEEE International Conference on Big Data, Washington DC, December 5-8, 2016
Enabling Stem Cell Characterization from Large Microscopy Images (pdf): Peter Bajcsy , Antoine Vandecreme, Julien Amelot, Joe Chalfoun, Michael Majurski, and Mary Brady
IEEE Computer, July, 2016
Methodology for Increasing the Measurement Accuracy of Image Features (pdf): Michael Majurski, Joe Chalfoun, Steven P. Lund, Peter Bajcsy, Mary Brady
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition Workshops. 2016.
Lineage mapper: A versatile cell and particle tracker (pdf): Joe Chalfoun, Michael Majurski, Alden Dima, Michael Halter, Kiran Bhadriraju, Mary Brady
Scientific Reports, 6, 2016.
Large-scale Time-lapse Microscopy of OCT-4 Expression in Human Embryonic Stem Cell Colonies (pdf): Kiran Bhadriraju, Michael Halter, Julien Amelot, Peter Bajcsy, Joe Chalfoun, Antoine Vandecreme, Barbara Mallon, Kye-yoon Park, Subhash, and Anne Plant
Elsevier Stem Cell Research, Volume 17, Issue 1, July 2016, Pages 122–129, DOI: 10.1016/j.scr.2016.05.012
Empirical Gradient Threshold Technique for Automated Segmentation across Image Modalities and Cell Lines (pdf): Joe Chalfoun, Michael Majurski, Adele Peskin, Catherine Breen, Peter Bajcsy and Mary Brady
Journal of Microscopy, 2015 Jun 5. doi: 10.1111/jmi.12269
Background Intensity Correction for Terabyte-Sized Time-Lapse Images (pdf): Joe Chalfoun, Michael Majurski, Kiran Bhadriraju, Steve Lund, Peter Bajcsy, Mary Brady
Journal of Microscopy, 2015, 257:226–238.
FogBank: a single cell segmentation across multiple cell lines and image modalities (pdf): Joe Chalfoun, Michael Majurski, Alden Dima, Christina Stuelten, Adele Peskin, Mary Brady
BMC Bioinformatics, 2014, 15:431.
Terabyte-sized Image Computations on Hadoop Cluster Platforms (pdf): Peter Bajcsy, Antoine Vandecreme, Julien Amelot, Phuong Nguyen, Joe Chalfoun, Mary Brady
IEEE International Conference on Big Data, October 6-9, 2013, Santa Clara, CA, USA
Re-projection of Terabyte-Sized Images (pdf): Peter Bajcsy, Antoine Vandecreme, Mary Brady
IEEE International Conference on Big Data, October 6-9, 2013, Santa Clara, CA, USA (poster)
Deep Zoom tool for advanced interactivity with high-resolution images (pdf): Paul Khouri-Saba, Antoine Vandecreme, Mary Brady and Peter Bajcsy
SPIE Newsroom, 24 May 2013, SPIE Newsroom. DOI: 10.1117/2.1201305.004866, https://spie.org/x93885.xml

3D Measurement of Stem Cells-Material Interactions

Effect of the Scaffold Microenvironment on Cell Polarizability and Capacitance Determined by Probabilistic Computations: Beatriz A. Pazmino Betancourt, Stephen J. Florczyk, Mylene Simon, Derek Juba, Jack F. Douglas, Walid Keyrouz, Peter Bajcsy, Christopher Lee and Carl G. Simon, Jr.
Biomedical Materials, BMM-101918.R1, Vol. 13, No. 2, pages 025012, Jan. 2018.
Modeling, Validation and Verification of Three-Dimensional Cell-Scaffold Contacts from Terabyte-sized Images: Peter Bajcsy, Soweon Yoon, Stephen Florczyk, Nathan Hotaling, Mylene Simon, Piotr Szczypinski, Nicholas Schaub, Carl Simon Jr., Mary Brady, and Ram Sriram
BMC Bioinformatics, November 2017; DOI 10.1186/s12859-017-1928-x;
A Bioinformatics 3D Cellular Morphotyping Strategy for Assessing Biomaterial Scaffold Niches: Stephen J. Florczyk, Mylene Simon, Derek Juba, P. Scott Pine, Sumona Sarkar, Desu Chen, Paula J. Baker, Subhadip Bodhak, Mary C. Brady, Peter Bajcsy*, and Carl G. Simon, Jr.*
ACS Biomaterials Science & Engineering, 2017 August, DOI: 10.1021/acsbiomaterials.7b00473;
A Method for the Evaluation of Thousands of Automated 3D Stem Cell Segmentations: Peter Bajcsy, Mylene Simon, Stephen Florczyk, Derek Juba, Carl Simon, and Mary Brady
Journal of Microscopy, 2015 Aug 13. doi: 10.1111/jmi.12303;

Material Science Applications

Interactive and Traceable Measurements over Terabyte-sized Images

From Image Tiles to Web-Based Interactive Measurements in One Stop (pdf): Antoine Vandecreme, Michael Majurski, Joe Chalfoun, Keana Scott, John Henry J. Scott, Mary Brady, Peter Bajcsy
Microscopy Today, 25.1, 2017.
Interactive Web-based Spatio-Statistical Image Modeling from Gigapixel Images to Improve Discovery and Traceability of Published Statistical Models (pdf): Peter Bajcsy, Antoine Vandecreme, and Mary Brady
Microscopy and Microanalyses conference, Columbus, Ohio. July 24-28, 2016.
From Image Tiles to Web-Based Interactive Measurements in One Stop (pdf): Antoine Vandecreme, Tim Blattner, Michael Majurski, Peter Bajcsy, Keana Scott, and John Henry J. Scott
Microscopy and Microanalyses conference, Portland, OR, August 2-6, 2015.

2D + Photon energy level Measurements of a Historical Artifact

Interactive Analysis of Terabyte-sized SEM-EDS Hyperspectral Images (pdf): Antoine Vandecreme, Peter Bajcsy, Nicholas W.M. Ritchie, and John Henry J. Scott
Microscopy and Microanalyses conference, Hartford, CT, August 3-7, 2014.
Microscopy image acquisition: D. E. Newbury and N. W. M. Ritchie
Elemental mapping of microstructures by scanning electron microscopy-energy dispersive X-ray spectrometry (SEM-EDS), J. Anal. At. Spectrom., vol. 28, no. 7, pp. 973-988, 2013.