VSR-SIM

VSR-SIM: Spatio-temporal Vision Transformer for Super-resolution Microscopy

Charles N. Christensen^1,2,*, Meng Lu¹, Edward N. Ward¹, Pietro Lio², Clemens F. Kaminski

¹University of Cambridge, Department of Chemical Engineering and Biotechnology, Laser Analytics Group
²University of Cambridge, Department of Computer Science and Technology, Artificial Intelligence Group
^*Author of this repository:

• GitHub: charlesnchr
• Email: charles.n.chr@gmail.com
• Twitter: charlesnchr

Introduction

Reconstruction method for Video Super-Resolution Structured Illumination Microscopy (VSR-SIM) using a vision transformer architecture.

The method is trained using synthesised video data based on a SIM image formation model and a dataset of nature documentaries for diverse and varied image data.

Being a video super-resolution method, VSR-SIM is inherently robust to significant levels of motion in input data as illustrated below.

VSR-SIM Publications

Journal Publication, 2022

Currently under review as of February 2022.

Pre-print manuscript, Feburary 2022

https://arxiv.org/abs/2203.00030

Layout of repository

• Powershell script for video dataset sampling:
  • scripts/sample_documentary_videos.ps1
• Python code for image formation model:
  • scripts/im_form_model/SIMulator.py
• Data generation script:
  • scripts/datagen_pipeline.py
• Model architecture based on Pytorch:
  • basicsr/archs/vsr-sim_arch.py
• Training code:
  • basicsr/train.py
• Inference code for testing:
  • inference/inference_options.py
• RBPN code base based on official implementation:
  • RBPN-PyTorch

Installation of environment

See requirements.txt for all the required packages. They can be installed with pip using

pip install -r requirements.txt

It is recommended to use Anaconda to make a virtual environment and for installation of Pytorch so that the CUDA drivers are installed automatically. The following snippet should install everything necessary:

conda create -n vsrsim python=3.8
conda activate vsrsim
conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch
pip install scikit-image matplotlib scipy opencv-python tqdm timm pyyaml einops torchsummary

Video sampling

Given a collection of .mp4 and .mkv video containers, we use the FFMPEG library to sample the collection with a time interval of 5 seconds between sequences. The script is launched using Powershell with

pwsh scripts/sample_documentary_videos.ps1

Data generation

The image formation pipeline can be used as follows

python datagen_pipeline.py --root TRAINING_DATA_DIRECTORY \
    --sourceimages_path SAMPLED_IMAGE_SEQUENCE_DIRECTORY --nrep 1\
    --datagen_workers 10 --imageSize 512  --nch_in 9 --nch_out 1\
    --ntrain 100000 --ntest 0 --scale 2 --nepoch 100 --scheduler 20,0.5\
    --norm minmax --workers 6 --dataonly --NoiseLevel 8 \
    --NoiseLevelRandFac 8 --Nangle 3 --Nshift 3 --phaseErrorFac 0.05 \
    --alphaErrorFac 0.05 --seqSIM --ext imagefolder

Training

To train a model with the VSR-SIM architecture using options specified in an associated options file, run the following

PYTHONPATH="./:${PYTHONPATH}" python basicsr/train.py \
    -opt options/train/VSR-SIM/VSR-SIM.yml

Inference on test set

Inference on a test set can be done with

PYTHONPATH="./:${PYTHONPATH}" python inference/inference_options.py\
    --task simrec --model_path experiments/VSR-SIM/models/net_g.pth\
    --scale 2 --input testdir/inputs --output testdir/outputs/VSR-SIM \
    -opt options/train/VSR-SIM/VSR-SIM.yml

Hyperparameters used in VSR-SIM and referenced methods

See Hyperparameters.md for an overview of the parameters used in models in the paper. The parameters are also given in the individual YAML files in the options folder.

Credits

The implementation of VSR-SIM and structure of the code is inspired by the following repositories. Reference implementations for methods that are compared to in the paper are also listed. See Hyperparameters.md for parameters used.

• SwinIR [@Liang2021]
  Reference implementation: SwinIR:
  https://github.com/JingyunLiang/SwinIR

• Video Swin [@Liu2021a]
  Reference implementation: Video-Swin-Transformer:
  https://github.com/SwinTransformer/Video-Swin-Transformer

• RBPN [@Haris2019]
  Reference implementation: RBPN-PyTorch:
  https://github.com/alterzero/RBPN-PyTorch

• RCAN [@Zhang2018d]
  Reference implementation: BasicSR [@wang2020basicsr]:
  https://github.com/xinntao/BasicSR