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:

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,

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.