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.
- 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 thejcuda
version being used.
- The version of
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
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 |
- 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.
- 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:
- Initialize the analysis server by sending
runcommand initialize $LOCATION_OF_WORKSPACE
to the analysis machine - Run the full evaluation by sending
runcommand evaluation $LOCATION_OF_TESTDATA 0 1
- The 4 angles that are optimal for image coverage can be queryed via
runcommand getupdate
- Initialize the analysis server by sending
The full evaluation should take around 2 mins depends on the speed of the filestorage.