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Bioimaging and microscopy

GDSPIKE: AN ACCURATE SPIKE ESTIMATION ALGORITHM FROM NOISY CALCIUM FLUORESCENCE SIGNALS


Accurate estimation of spike train from calcium (Ca2+) fluorescence signals is challenging owing to significant fluctuations of fluorescence level. This paper proposes a non-model-based approach for spike train inference using group delay (GD) analysis. It primarily exploits the property that change in Ca2+ fluorescence corresponding to a spike can be characterized by an onset, an attack, and a decay. The proposed algorithm, GDspike, is compared with state-of-the-art systems on five datasets. F-measure is best for GDspike (41%) followed by STM (40%), MLspike (39%), and Vogelstein (35%).

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Authors:
Jilt Sebastian, Mari Ganesh Kumar, Y. S. Sreekar, Rajeev Vijay Rikhye, Mriganka Sur, Hema A. Murthy
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7 March 2017 - 1:28pm
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[1] Jilt Sebastian, Mari Ganesh Kumar, Y. S. Sreekar, Rajeev Vijay Rikhye, Mriganka Sur, Hema A. Murthy, " GDSPIKE: AN ACCURATE SPIKE ESTIMATION ALGORITHM FROM NOISY CALCIUM FLUORESCENCE SIGNALS", IEEE SigPort, 2017. [Online]. Available: http://sigport.org/1690. Accessed: May. 30, 2017.
@article{1690-17,
url = {http://sigport.org/1690},
author = {Jilt Sebastian; Mari Ganesh Kumar; Y. S. Sreekar; Rajeev Vijay Rikhye; Mriganka Sur; Hema A. Murthy },
publisher = {IEEE SigPort},
title = { GDSPIKE: AN ACCURATE SPIKE ESTIMATION ALGORITHM FROM NOISY CALCIUM FLUORESCENCE SIGNALS},
year = {2017} }
TY - EJOUR
T1 - GDSPIKE: AN ACCURATE SPIKE ESTIMATION ALGORITHM FROM NOISY CALCIUM FLUORESCENCE SIGNALS
AU - Jilt Sebastian; Mari Ganesh Kumar; Y. S. Sreekar; Rajeev Vijay Rikhye; Mriganka Sur; Hema A. Murthy
PY - 2017
PB - IEEE SigPort
UR - http://sigport.org/1690
ER -
Jilt Sebastian, Mari Ganesh Kumar, Y. S. Sreekar, Rajeev Vijay Rikhye, Mriganka Sur, Hema A. Murthy. (2017). GDSPIKE: AN ACCURATE SPIKE ESTIMATION ALGORITHM FROM NOISY CALCIUM FLUORESCENCE SIGNALS. IEEE SigPort. http://sigport.org/1690
Jilt Sebastian, Mari Ganesh Kumar, Y. S. Sreekar, Rajeev Vijay Rikhye, Mriganka Sur, Hema A. Murthy, 2017. GDSPIKE: AN ACCURATE SPIKE ESTIMATION ALGORITHM FROM NOISY CALCIUM FLUORESCENCE SIGNALS. Available at: http://sigport.org/1690.
Jilt Sebastian, Mari Ganesh Kumar, Y. S. Sreekar, Rajeev Vijay Rikhye, Mriganka Sur, Hema A. Murthy. (2017). " GDSPIKE: AN ACCURATE SPIKE ESTIMATION ALGORITHM FROM NOISY CALCIUM FLUORESCENCE SIGNALS." Web.
1. Jilt Sebastian, Mari Ganesh Kumar, Y. S. Sreekar, Rajeev Vijay Rikhye, Mriganka Sur, Hema A. Murthy. GDSPIKE: AN ACCURATE SPIKE ESTIMATION ALGORITHM FROM NOISY CALCIUM FLUORESCENCE SIGNALS [Internet]. IEEE SigPort; 2017. Available from : http://sigport.org/1690

ICASSP_poster_Paper_1008


This paper proposes a reliable 3D fish tracking method using a novel master-slave camera setup. Instead of conventional dynamic models that rely on prior knowledge about target kinematics, the proposed method learns the kinematic model with a Long Short-Term Memory (LSTM) network. On this basis, the 3D state of fish at each moment is predicted by LSTM network. We propose to use an innovative master-view-tracking-first strategy. The fish are first tracked in the master view. Cross-view association is then established utilizing motion continuity and epipolar constraint cues.

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Authors:
Shuo Hong Wang, Jingwen Zhao, Xiang Liu, Zhi-Ming Qian, Ye Liu, Yan Qiu Chen
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1 March 2017 - 10:13am
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[1] Shuo Hong Wang, Jingwen Zhao, Xiang Liu, Zhi-Ming Qian, Ye Liu, Yan Qiu Chen, "ICASSP_poster_Paper_1008", IEEE SigPort, 2017. [Online]. Available: http://sigport.org/1537. Accessed: May. 30, 2017.
@article{1537-17,
url = {http://sigport.org/1537},
author = {Shuo Hong Wang; Jingwen Zhao; Xiang Liu; Zhi-Ming Qian; Ye Liu; Yan Qiu Chen },
publisher = {IEEE SigPort},
title = {ICASSP_poster_Paper_1008},
year = {2017} }
TY - EJOUR
T1 - ICASSP_poster_Paper_1008
AU - Shuo Hong Wang; Jingwen Zhao; Xiang Liu; Zhi-Ming Qian; Ye Liu; Yan Qiu Chen
PY - 2017
PB - IEEE SigPort
UR - http://sigport.org/1537
ER -
Shuo Hong Wang, Jingwen Zhao, Xiang Liu, Zhi-Ming Qian, Ye Liu, Yan Qiu Chen. (2017). ICASSP_poster_Paper_1008. IEEE SigPort. http://sigport.org/1537
Shuo Hong Wang, Jingwen Zhao, Xiang Liu, Zhi-Ming Qian, Ye Liu, Yan Qiu Chen, 2017. ICASSP_poster_Paper_1008. Available at: http://sigport.org/1537.
Shuo Hong Wang, Jingwen Zhao, Xiang Liu, Zhi-Ming Qian, Ye Liu, Yan Qiu Chen. (2017). "ICASSP_poster_Paper_1008." Web.
1. Shuo Hong Wang, Jingwen Zhao, Xiang Liu, Zhi-Ming Qian, Ye Liu, Yan Qiu Chen. ICASSP_poster_Paper_1008 [Internet]. IEEE SigPort; 2017. Available from : http://sigport.org/1537

A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows


Image Stitching Hybrid Task Graph

The scalability of applications is a key requirement to improving performance in hybrid and cluster computing. Scheduling code to utilize parallelism is difficult, particularly when dealing with dependencies, memory management, data motion, and processor occupancy. The Hybrid Task Graph Scheduler (HTGS) increases programmer productivity to implement hybrid workflows that scale to multi-GPU systems.

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Authors:
Walid Keyrouz, Milton Halem, Shuvra Bhattacharyya, Mary Brady
Submitted On:
23 February 2016 - 1:44pm
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GlobalSIP-Hybrid Task Graph Scheduler.pptx

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[1] Walid Keyrouz, Milton Halem, Shuvra Bhattacharyya, Mary Brady, "A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows", IEEE SigPort, 2015. [Online]. Available: http://sigport.org/451. Accessed: May. 30, 2017.
@article{451-15,
url = {http://sigport.org/451},
author = {Walid Keyrouz; Milton Halem; Shuvra Bhattacharyya; Mary Brady },
publisher = {IEEE SigPort},
title = {A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows},
year = {2015} }
TY - EJOUR
T1 - A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows
AU - Walid Keyrouz; Milton Halem; Shuvra Bhattacharyya; Mary Brady
PY - 2015
PB - IEEE SigPort
UR - http://sigport.org/451
ER -
Walid Keyrouz, Milton Halem, Shuvra Bhattacharyya, Mary Brady. (2015). A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows. IEEE SigPort. http://sigport.org/451
Walid Keyrouz, Milton Halem, Shuvra Bhattacharyya, Mary Brady, 2015. A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows. Available at: http://sigport.org/451.
Walid Keyrouz, Milton Halem, Shuvra Bhattacharyya, Mary Brady. (2015). "A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows." Web.
1. Walid Keyrouz, Milton Halem, Shuvra Bhattacharyya, Mary Brady. A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows [Internet]. IEEE SigPort; 2015. Available from : http://sigport.org/451

A Multi-Frame Optical Flow Spot Tracker


Stationary Motion Estimation

Accurate and robust spot tracking is a necessary tool for quantitative motion analysis in fluorescence microscopy images. In this work, we exploits the underlying stationary motion in biological systems, e.g. the movement of crowds, bacteria swarming and cyclosis in plant cells, and then propose a multi-frame optical flow based tracker. We obtain the stationary motion by adapting a recent optical flow algorithm that relates one image to another locally using an all-pass filter.

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Authors:
Christopher Gilliam, Thierry Blu
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23 February 2016 - 1:38pm
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ICIP2015_poster_SLAPTracker.pdf

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[1] Christopher Gilliam, Thierry Blu, "A Multi-Frame Optical Flow Spot Tracker", IEEE SigPort, 2015. [Online]. Available: http://sigport.org/225. Accessed: May. 30, 2017.
@article{225-15,
url = {http://sigport.org/225},
author = {Christopher Gilliam; Thierry Blu },
publisher = {IEEE SigPort},
title = {A Multi-Frame Optical Flow Spot Tracker},
year = {2015} }
TY - EJOUR
T1 - A Multi-Frame Optical Flow Spot Tracker
AU - Christopher Gilliam; Thierry Blu
PY - 2015
PB - IEEE SigPort
UR - http://sigport.org/225
ER -
Christopher Gilliam, Thierry Blu. (2015). A Multi-Frame Optical Flow Spot Tracker. IEEE SigPort. http://sigport.org/225
Christopher Gilliam, Thierry Blu, 2015. A Multi-Frame Optical Flow Spot Tracker. Available at: http://sigport.org/225.
Christopher Gilliam, Thierry Blu. (2015). "A Multi-Frame Optical Flow Spot Tracker." Web.
1. Christopher Gilliam, Thierry Blu. A Multi-Frame Optical Flow Spot Tracker [Internet]. IEEE SigPort; 2015. Available from : http://sigport.org/225