Wednesday: October 14, 2015

1:00pm – 1:10pm

Welcome by the ITL director, Dr. Charles Romine

1:10pm – 1:20pm

Opening remarks by the conference chair, Dr. Peter Bajcsy

1:20pm – 2:20pm

Keynote: Dr. Winfried Denk, Max Planck Institute of Neurobiology; Towards a circuit diagram of the brain

2:20pm – 2:50pm

Coffee Break

2:50pm – 3:30pm

Session 1 (2x 20 min): Brain Imaging Chair: John Elliott, NIST

Roysam B: Comprehensive Mapping of Cellular Alterations in Brain Tissue.

Peng H., BigNeuron Project

3:30pm – 4:00pm

Coffee Break

4:00pm – 5:00pm

Session 2 (3x 20 min): Large Scale Image Analyses Chair: Antonio Cardone, University of Maryland at College Park

Pietzsch, T., Preibisch, S., Saalfeld, S., & Tomancak, P. BigDataViewer: Visualization and Image Processing for Terabyte Data Sets

Kumar VS, Williams JW, Aggour KS, Sarachan B, Al-Kofahi Y, Santamaria-Pang A: Collaborative Analysis of High-Content Image Data.

Economo, M. N., Clack, N. G., Arthur, B. J., Bruns, C., & Chandrashekar, J. (2015). Registration and visualization of large-scale 3D mosaic images.

5:00pm – 6:00pm

Transportation to hotel


Thursday: October 15, 2015

8.30am – 8:40am

Announcements: BII2016 in Singapore and Call for BII2017 proposals

8.40am – 9:40am

Keynote: Dr. Ivo Sbalzarini, Max Planck Institute of Molecular Cell Biology and Genetics; Model-based Image Analysis for Fluorescence Microscopy

9:40am – 10:00am


10:00am – 11:00am

Session 3 (4 x 15 min): Cell Imaging Chair: Michael Halter, NIST

Yi J, Barr V, Manna AK, Hong J, Neuman KC, Samelson LE: Signaling Microclusters in T cells.

Camp, C. H., Lee, Y. J., & Cicerone, M. T. : Quantitative , Comparable Hyperspectral Chemical Imaging of Biological Specimens with Broadband Coherent Anti-Stokes Raman Scattering ( BCARS ) Microspectroscopy.

Joshi R, Swaminathan SR, Winter M, Saini JS, Blenkinsop TA, Stern J, Temple S, Cohen AR: Measuring visual structure in phase and fluorescence microscopy using image compression.

Traver M, Schaefer B, Campanello L, Losert W, Shroff H: Mechanisms of T Lymphocyte Activation Revealed by Super-Resolution Microscopy.

11:00am – 11:20am

Coffee Break

11:20am – 12:30am

Parallel Sessions 4 (60 min presentations and 10 min discussion per session): Conference Challenges

Stitching Challenge in Green Auditorium Chaired by Joe Chalfoun, NIST

·         Chalfoun J.: Stitching Challenge - Evaluation Methodology

·         Sun, C.: Stitching Challenge: CSIRO-QI.

·         Wait, E., Winter, M., & Cohen, A.: Stitching Challenge: Normalized Covariance Image Stitching Technique for Rigid Registration of Microscope Tiles.

·         Yang, G. Stitching Challenge: i2k Align v3.0.

·         Wang, C.-W.: Stitching Challenge: Linear Blending.

·         Discussion

Cell Nucleus Counting Challenge in Lecture Room A: Chaired by Maric Dragan, NIH

·         Maric D.: Nucleus Counting Challenge: Nucleus counting in brain immune-histology applications: A crucial requirement to study tissue remodeling after ischemic and traumatic brain injury.

·         Wang C. & Yu G.: Nucleus Counting Challenge Method

·         Discussion

12:30pm – 2:00pm

Lunch and Poster Session

2:00pm – 3:00pm

Keynote: Stephen Smith, Allen Institute of Brain Science, Toward Photonic Connectomes

3:00pm – 3:30pm

Coffee Break

3:30pm – 4:30pm

Session 5 (4 x 15 min): Cell Image Analyses Chair: Andrew Cohen, Drexel University

Hirose O, Kawaguchi S, Tokunga T, Teramoto T, Kuge S, Ishihara T, Toyoshima Y, Iino Y, Yoshida R: SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter.

Mankowski WC, Konica G, Winter MR, Chen F, Maus C, Merkle R, Klingmuller U, Hofer T, Kan A, Heinzel S, Oostindie S, Hodgkin P, Cohen AR: Multi-Modal Segmentation for Quantifying Fluorescent Cell Cycle Indicators Throughout Clonal Development.

Matuszewski DJ, Sintorn IM, Puigvert JC, Wahlby C: Comparing cell cycle analysis using flow cytometry and image-based screening.

Kwee, E., Powel, K., & Muschler, G.: Characterization of connective tissue progenitors through phase contrast and multicolor fluorescence time-lapse microscopy

4:30pm – 5:30pm

Transportation to hotel


Banquet at the hotel location



Friday: October 16, 2015

8.30am – 9:30am

Keynote: Dr. Jean-Karim Hιrichι, European Molecular Biology Laboratory; Building a canonical model of the human mitotic cell

9:30am – 9:50am


9:50am – 10:50am

Session 6 (4 x 15 min): Morphology Analyses Chair: Carl Simon, NIST

Singh S: Morphological Profiling for Targeting Diseases and Characterizing Compounds.

Florczyk SF, Baker P, Bodhak S, Juba D, Cardone A, Pine PS, Brady M, Sarkar S, Bajcsy P, Chen D, Simon CG: 3D Cellular Morphotyping of Scaffold Niches.

Goldberg IG: Pattern recognition with markerless, stain-free, non-destructive imaging.

Bartholomew, A., Szilagyi, E., Patil, R., Premand, K., & Yu, J.: The Need for Highly Sensitive Imaging as a Rapid Functional Test of Mesenchymal Stem Cell (MSC) Therapeutics.

10:50am – 11:10am

Coffee Break

11:10am – 12:10am

Session 7 (4x 15 min): BigNeuron and Neuron Reconstruction Chair: Hanchuan Peng, Allen Institute for Brain Science

Chen H.: High-throughput color-separation of neurons in BigNeuron

Gu L. and Cheng L.: Learning to Improve Single Neuron Segmentation

Wang C-W.: Automatic tracing and registration of multi-dimensional microscopic images in high resolution

Zhao T.: Neuron Tracing Methods in NeuTu

Zhou, J. Toward 3D Synaptic Distributed Analysis with Neuron Reconstruction.

12:10pm – 1:00pm


1:00pm – 2:00pm

Session 8 (4 x 15 min): Large Scale Image Visualization Chair: Peter Bajcsy, NIST

Torosdagli N, Pattanaik S, Lisle C, Liu Y: Web based Out-of-Core Volume Visualization in Client-Server Architectures.

Wait E, Winter M, Song S, Monteleone D, Cohen A, Bjornsson CF, Goderie S, Temple S: Collaborative Visualization in the Browser for Segmentation , Tracking , and Lineaging with 5-D Biological Microscopy Images.

Harrington KIS, Stiles TS, Venkatraman L, Prahst, C, Bentley K: Functional Image Processing with ImageJ/FIJI.

Cardona A.: Quantitative Cellular Neuroanatomy as the Foundation for Mapping Neural Circuits from Electron Microscopy

2:00pm – 3:00pm

Session 9 (4 x 15 min): Machine Learning Chair: Jana Kosecka, George Mason University

Wang Y, Wang Y, Yu G, Shi G, Tian L: PPSD : Probability Principled Synapse Detection.

Rajabi Z, Kosecka J, Bajcsy P: Confidence Estimation in Stem Cell Classification.

Ji S: Deep Learning for Bioimage Informatics.

Gu L, Chen L: Learning to Boost Filamentary Structure Segmentation.

3:00pm – 3:30pm

Coffee Break

3:30pm – 4:15pm

Session 10 (3x 15 min): Microscopy Image Analysis Environments Chair: Charles Camp, NIST

Nandy K, Liu Y, Mott D, Meaburn K, Misteli T, Lockett SJ, Gudla PR: MiPipeline ( Microscopy Pipeline ): A User Friendly Software Environment for Microscopy Image Analysis and Informatics.

Carrol MG, Swedlow JR: The Open Microscopy Environment : Open Source Image Informatics for the Biological Sciences.

Xiao M, Zou C, Sheppard K, Krebs M: OCT Image Stack Alignment: one more important preprocessing step.

4:15pm – 4:20pm

Closing remarks by the conference chair, Dr. Peter Bajcsy

4:20pm – 5:20pm

Transportation to hotel



Thursday after lunch: Poster Session

Poster IDs are below

Poster presentations

1.      Cardone A, Kociolek M, Brady M, Bajcsy P: Estimating Actin Fiber Orientation using Interpolation-Based Gray-Level Co-Occurrence Matrix Computation. In BioImage Informatics conference; 2015.

2.      Cardone A, Kociolek M, Chalfoun J, Bhadriraju K, Peskin A, Brady M, Bajcsy P: Segmentation and feature-based analysis of sub-cellular microscopy images. In BioImage Informatics conference; 2015.

3.      Chen D, Candia J, Driscoll MK, Losert W, Sarkar S, Florczyk SJ, Bodhak S, Simon CG, Dunkers JP: Machine Learning Based Methodology to Identify Cell Shape Phenotypes Associated with Microenvironmental Cues. In BioImage Informatics conference; 2015:6–8.

4.      Coletta CE, Goldberg IG: The WND-CHARM Python API Pythonic Pattern Recognition for Bioimage Informatics. In BioImage Informatics conference; 2015:5.

5.      De J, Cheng L, Lin F: Tracing Filamentary Structures in Neuronal Images. In BioImage Informatics conference; 2015:1–4.

6.      Litorja M, Samarov D: Use of Image Segmentation Algorithm to Test Model Spectral Distribution for Surgical Lighting. In BioImage Informatics conference; 2015.

7.      Majurski M, Zheng C, Chalfoun J, Dima A, Brady M: Shape Descriptors Comparison for Cell Tracking. In BioImage Informatics conference; 2015:1–4.

8.      Ranefall P, Wahlby C: Your New Default Thresholding Method ? A robust global gray-level thresholding method based on object features. In BioImage Informatics conference; 2015.

9.      Shen Y, Losert W, Candia J, Morozov A: Automated analysis pipeline for high throughput screening data on the single cell level. In BioImage Informatics conference; 2015.

10.  Shirtz AE, Koos DS, Pollack H, Moats R, Warburton D: Extended Volume Creation in Z Using Speeded Up Robust Features. In BioImage Informatics conference; 2015:2–4.

11.  Zhou J, Yang L, Ye B: QTIP : Quantifier for Topographic Index of Presynaptic-terminal using 3D Confocal Imaging. In BioImage Informatics conference; 2015.

12.  Pietzsch, T., Preibisch, S., Saalfeld, S. & Tomancak, P. BigDataViewer: Visualization and Image Processing for Terabyte Data Sets. in BioImage Informatics Conf. 2015.

13.  Chalfoun, J., Majurski, M., Blattner, T., Keyrouz, W., Bajcsy, P., & Brady, M.: MIST: Microscopy Image Stitching Tool. In BioImage Informatics Conf. 2015.

14.  Simon, M., Florczyk, S.J., Juba, D., Baker, P.J., Simon, C.G.J., Brady, M., & Bajcsy, P.: Segmentation of Large Numbers of 3D Cells on Different Scaffolds. In BioImage Informatics Conf. 2015.

15.  Vandecreme, A., Majurski, M., Chalfoun, J., Scott, K., Scott, J.H.J., Brady, M., & Bajcsy, P.: From Image Tiles to Web-Based Interactive Measurements. In BioImage Informatics Conf. 2015.

16.   Juba, D., Cyrus T., & Keyrouz, W.: Cell Visualization on a Desktop Display Wall. In BioImage Informatics Conf. 2015.

17.      Tohsato, Y., Kyoda, K., Ho, K.H.L., & Onami, S.: SSBD: An Integrated Database of Quantitative Data and Microscopy Images of Biological Dynamics. In BioImage Informatics conference; 2015.

18.      Dogan, G., Bernal, J., & Hagwood, C.R.: Fast Computation of Elastic Shape Distance between 2d Objects. In BioImage Informatics conference; 2015.

19.      Elliott, J., Cooksey, G., & Plant, A.: Developing Image-Based Measurements to Characterize Stem Cells Cultured as Colonies. In BioImage Informatics conference; 2015.

20.      Dogan, G.: A Python Toolbox for Shape Detection and Analysis in Images. In BioImage Informatics conference; 2015.

21.      Halter, M., Bier, E., DeRose, P.C., Cooksey, G.A., Choquette, S.J., Plant, A.L., & Elliott, J.T.: Performance Benchmarking a Widefield Fluorescence Microscope Using Fluorescent Glass. In BioImage Informatics conference; 2015.

22.      Halter, M., Lund, S., Li-Baboud, Y.-S., Peskin, A.P., Bajcsy, P., Hoeppner, D.J., & Plant, A.L.: Reducing Uncertainty in the Evaluation of Stem Cell Colonies. In BioImage Informatics conference; 2015.

23.      Baker, P. J., Lin, N. J., Pintar, A. L., Lin-Gibson, S. & Lopez-Perez, D.: Evaluating the Activity of an Anti-biofilm Agent via Imaging In BioImage Informatics conference; 2015.

24.      Schaub, N. J., Halter, M., Hotaling, N., Bharti, K. & Simon, C. A Simple: Robust Microscopy Method for Quantifying Absorption. In BioImage Informatics conference; 2015.

25.      Peterson, A. W., Halter, M., Tona, A., Bhadriraju, K., Elliott, J. T., & Plant, A. L., . In BioImage Informatics Conf. 2015. High Resolution Surface Plasmon Resonance Imaging of Focal Adhesions in Single Cells. In BioImage Informatics conference; 2015.