Journal Clubs

Journal clubs are held in the STIM Laboratory (W309). For each session, a participating student or researcher will select a relevant paper, send that paper to the group, and present it for discussion. The number of sessions will depend on the number of participants, with the goal of each student presenting 1-2 papers per year.

Microscopy and Microscope Image Processing

Mondays at 11am - 12pm (STIM Laboratory - Engineering Building 2, W309)

This journal club focuses on the hardware and algorithms for acquiring and processing high-resolution images. Based on the interests of the labs involved, presented papers will generally focus on large biomedical images collected using optical microscopy, including bright-field, fluorescence, and infrared imaging.

Relevant topics include: new imaging techniques, three-dimensional imaging, image processing, segmentation, hyperspectral image analysis, noise removal, and reconstruction

Date Presenter Paper
 5/23 Xiaoyang Li Development of a memetic clustering algorithm for optimal spectral histology: application to FTIR images of normal human colon
6/13 Shihao Ran Three-dimensional IR imaging with uncooled GaN photodiodes using nondegenerate two-photon absorption
6/20 Boris Penaloza Performance-optimized hierarchical models predict neural responses in higher visual cortex
 8/1 Davar Image Processing and Analysis for Single-Molecule Localization Microscopy: Computation for nanoscale imaging
 8/15 Tasha Womack High-throughput 3D whole-brain quantitative histopathology in rodents
 Srijani Mukherjee  Line-scan Raman microscopy complements optical coherence tomography for tumor boundary detection
Sample Papers / Journals

"Expansion microscopy with conventional antibodies and fluorescent proteins."
Nature Methods (2016)

Chozinski, Halpern, Okawa, Kim, Tremel, Wong, and Vaughan

"Fast 3D visualization of endogenous brain signals with high-sensitivity laser scanning photothermal microscopy."
Biomedical Optics Express (2016)

Miyazaki, Iida, Tanaka, Hayashi-Takagi, Kasai, Okabe, and Kobayashi

"Hermite Snakes with Control of Tangents."
IEEE Transactions on Image Processing (2016)

Uhlmann, Fageot, and Unser

"NeuroBlocks: Visual Tracking of Segmentation and Proof-Reading for Large Connectomics Projects"
IEEE Transactions on Visualization and Computer Graphics (2016)

Ai-Awami, Beyer, Haehn, Kasthuri, Lichtman, Pfister, and Hadwiger

GPU Programming

Wednesdays at 4pm - 5pm (STIM Laboratory - Engineering Building 2, W309)

This journal club will focus on high-performance heterogeneous computing, with a particular focus on highly parallel architectures such as GPUs and the Xeon Phi. We expect the audience to be primarily electrical engineers with some understanding of the underlying GPU architecture.

Relevant topics include: new GPU architectures, GPU-based algorithms, heterogeneous algorithms, CUDA

Date Presenter Paper
5/18 Kedar Grama Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks
Srijani Mukherjee Edge-Preserving Image Denoising via Group Coordinate Descent on the GPU
Sample Papers / Journals

"GeePS: Scalable deep learning on distributed GPUs with a GPU-specialized parameter server."
Proceedings of the Neural Information Professing Systems Conference (NIPS) (2016)

Ren, He, Girshick, and Sun

"Edge-Preserving Image Denoising via Group Coordinate Descent on the GPU."
IEEE Transactions on Image Processing (2016)

McGaffin and Fessler

"GPU-Based Fuzzy C-Means Clustering Algorithm for Image Segmentation."
arXive (2016)

Almazrooie, Vadiveloo, and Abdullah

"A parallel adaptive segmentation method based on SOM and GPU with application to MRI image processing."
Neurocomputing (2016)

De, Zhang, and Guo

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