Smart Rotation workflow software

Smart Rotation workflow software is used to intelligently analyse a multi-view dataset and select the best view combination that gives the optimal imaging response.

Requirements:

• 64-bit operating System (Linux or Windows)
• CUDA 9.0.176 driver installed on an analysis computer
  • The version of CUDA driver required is determined by the jcuda version being used.
• CUDA enabled graphics card with at least 4GB of VRAM
  • VRAM size dictates the size of Z-STACK that can be analysed.
• A TCP/IP connection from the microscope to the analysis computer

Tested hardware:

Graphics card	Operating System
NVIDIA Quadro M5000	Windows 10
NVIDIA Quadro M5000	Windows Server 2016
NVIDIA Titan	Ubuntu 16.4
NVIDIA Quadro P5000	Centos 7

Installation:

• Download the content of the repository to the machine that is running the analysis server.
• Follow the instruction from the instruction.txt to configure the server and client.

Demo:

• Download the demo data file from [https://uwmadison.box.com/s/lswqqiok2t883kth5me8195ybxk43872]
• The demo data includes a 24-view dataset of a zebrafish embryo with histone nucleus labelling
• Start the analysis server by running `run "java -jar SmartRotationProcessing.jar $server_config". $server_config is the location of the server configuration file. See server_config.txt for sample usage.
• Run the full 24-angle evaluation on the dataset:
  1. Initialize the analysis server by sending runcommand initialize $LOCATION_OF_WORKSPACE to the analysis machine
  2. Run the full evaluation by sending runcommand evaluation $LOCATION_OF_TESTDATA 0 1
  3. The 4 angles that are optimal for image coverage can be queryed via runcommand getupdate

The full evaluation should take around 2 mins depends on the speed of the filestorage.