Research Programming & Computational Analysis Core

Downs crawford3 RGrytz calvert blank person Liyan Gao
Core Director
Crawford Downs, PhD
cdowns@uab.edu
Associate Core Director
Rafael Grytz, PhD
grytz@uab.edu
Laboratory Manager
Chester Calvert 

chesterc@uab.edu
Image Analysis
Scientist 1 
William Warriner, PhD
wwarr@uab.edu
Database Analyst
Liyan Gao, PhD
gaoly@uab.edu
 

 

Location & Contact
VH L-106-C / VH L-106-E
Phone: (205) 215-3868
opencl logo    cplusplus    Java Logo  
Matlab Logo     Labview logo 
adobe flash    php logo   MySQL
 New Guidelines for Core Usage to Minimize COVID-19 Infection
  • For new projects, the investigator will describe the needed project in programming/research hardware interfacing/data acquisition (Chester), image analysis (William) or database design/programming (Liyan) and provide detailed direction regarding desired outcomes.
  • Chester Calvert will communicate with Core members regarding new projects by email, videoconference, or phone. Please contact him at chesterc@uab.edu to discuss projects or arrange a video or phone conference.
  • William Warriner will communicate with Core members regarding new projects by email, videoconference, or phone. Please contact him at wwarr@uab.edu to discuss projects or arrange a video or phone conference.
  • Database management services are provided with assistance from Liyan Gao who will communicate with Core members regarding new projects by email, videoconference, or phone. Please contact her at gaoly@uab.edu to discuss projects or arrange a video or phone conference.
  • RPCA Core personnel will continue to coordinate and communicate with Core users as needed until project completion.

PPE, Social Distancing and Disinfecting Requirements

It is believed that almost all services provided by the Research Programming & Computational Analysis Core can be done remotely. If at any time it is necessary to meet in person or have an RPCA visit a Core member’s laboratory, all parties involved must wear a face mask and maintain a 6-foot separation where possible.


 

Projects 
Manuals
   

 

The Research Programming & Computational Analysis Core offers researchers a comprehensive programming and image analysis service where custom image analysis routines and standalone programs can be developed for individual project needs by highly trained personnel. The Core also develops the control software that allows custom instrumentation to be interfaced with computers in the laboratory setting, which is typically achieved using LabVIEW, Java, C, C++, Matlab, and other languages   ZStim GUI
    User interface of one of the completed and actively supported instrument control systems


The main goal of the Research Programming & Computational Analysis Core is to provide assistance in configuring software and hardware to ensure that computer equipment meets all requirements for proper execution of vision science experiments and other research related activities. The Research Programming & Computational Analysis Core works closely with investigators and collaborates with other cores to design and develop custom commercially unavailable software required to manage experimental equipment, to process experiment data.

Services include:
  • Development of custom, specialized software
  • Development of customized hardware/software interfaces and instrument control systems
  • Website authoring, hosting and development of web applications
  • Development and maintenance of online scheduling services for shared instrumentation

Advanced Programming and Computational Analysis (William Warriner)
William is a scientist with both a pure mathematics and engineering background with 6 years experience designing and developing 2D, 3D and 4D image analysis pipelines and workflows. He is skilled with data analysis, machine learning and deep learning tools and techniques, including visualizations and GUI and user experience development. He has experience applying these tools to image, tabular, mesh and signal data. He has expertise with MATLAB, Python, R, C++ and SQL programming, and with transforming applications for use with the UAB high performance computing cluster Cheaha using Bash and the SLURM job scheduler. William is able to efficiently identify when to use existing tools, when to re-engineer those tools for a niche task, or develop entirely new tools for new problems. William is familiar with software development tools including Visual Studio, VS Code, MATLAB, Anaconda, Git and GitHub and GitLab, and Docker and Singularity, but welcomes new tools and methodologies.

Some Recent and Upcoming Projects:

- Dr. Massimo Fazio (complete): Transitioning Mathematica deep learning workflows to Cheaha cluster

 - Dr. Christine Curcio: Hyperspectral autofluorescence spectral decomposition pipeline

 - Dr. Steven Pittler: Hardware interface between RGB camera and MicroManager software

 - Dr. Steven Pittler: OMERO server instance installation

 - Dr. Steven Pittler: OCT file format conversion utility

 - Dr. Kristina Visscher: Robust and replicable tracking of eye movements in MRI scanner

 - Dr. Crawford Downs: Human ONH delineation GUI for mechanical modeling

 - Dr. Rafael Grytz: Tree Shrew ONH delineation GUI, orientation and strain analysis pipeline

 - Dr. Cynthia Owsley (upcoming): Retinal fundus vasculature segmentation

 - Dr. Cynthia Owsley (upcoming): Automated longitudinal cross-modal image registration

 - Dr. Cynthia Owsley (upcoming): Co-registration of 3D OCT scans with 2D fundus photography


 Other Recent Projects. Follow the link to see more information on software development and other projects

Posters presented at UAB Core Day
VSRC Cores 2014
VSRC Research Programming and Computational Analysis Core 2014

Equipment

MacPro, Work Stations, Linux Servers, Color Scanner, Color Laser Printer, Slide/Film Scanner