Software and algorithms |
|
MARS-Net |
This paper |
https://github.com/kleelab-bch/MARS-Net |
ImageJ |
Schneider et al. (2012) |
https://imagej.nih.gov/ij/ |
MATLAB 2019b–2021b |
MathWorks |
https://www.mathworks.com/products/matlab.html |
Python 3.6.8 |
Python Software Foundation |
https://www.python.org/ |
Anaconda v4.5.11 |
Anaconda |
https://www.anaconda.com/ |
CUDA v10.1 |
NVIDIA |
https://developer.nvidia.com/cuda-toolkit |
cuDNN v7.6.5 |
NVIDIA |
https://developer.nvidia.com/rdp/cudnn-archive |
Extended Berkeley Segmentation Benchmark |
David Stutz |
https://github.com/davidstutz/extended-berkeley-segmentation-benchmark |
Windowing and Protrusion Package |
Gaudenz Danuser Lab |
https://github.com/DanuserLab/Windowing-Protrusion |
npy-matlab |
Kwik Team |
https://github.com/kwikteam/npy-matlab |
TensorFlow v2.3 |
TensorFlow |
https://www.tensorflow.org/ |
Matplotlib v3.3.4 |
Matplotlib |
https://matplotlib.org/ |
NumPy v1.18.5 |
NumPy |
https://numpy.org/ |
Absl-py (v0.12.0) |
Abseil Python Common Libraries |
https://github.com/abseil/abseil-py |
Grpcio (v1.37.0) |
The gRPC Authors |
https://pypi.org/project/grpcio/ |
H5py (v2.10.0) |
Andrew Collette and contributors |
https://www.h5py.org/ |
Imageio (v2.9.0) |
Imageio |
https://imageio.readthedocs.io/en/stable/ |
Importlib-metadata (v3.10.0) |
Python |
https://docs.python.org/3/library/importlib.metadata.html |
Joblib (v1.0.1) |
Joblib |
https://joblib.readthedocs.io/en/latest/ |
Keras-preprocessing (v1.1.2) |
TensorFlow |
https://www.tensorflow.org/api_docs/python/tf/keras/preprocessing |
Numba (v0.53.1) |
Numba |
https://numba.pydata.org/ |
OpenCV-contrib-python (v4.5.1.48) |
OpenCV |
https://docs.opencv.org/4.x/d6/d00/tutorial_py_root.html |
OpenCV-python (v4.5.1.48) |
OpenCV |
https://docs.opencv.org/4.x/d6/d00/tutorial_py_root.html |
Pillow (v8.2.0) |
Tidelift |
https://github.com/python-pillow/Pillow |
Psutil (v5.8.0) |
Giampaolo Rodola |
https://github.com/giampaolo/psutil |
Scikit-image (v0.17.2) |
scikit-image |
https://scikit-image.org/ |
Scikit-learn (v0.24.1) |
scikit-learn |
https://scikit-learn.org/stable/ |
Scipy (v1.4.1) |
SciPy |
https://scipy.org/ |
Tqdm (v4.60.0) |
Casper da Costa-Luis |
https://github.com/tqdm/tqdm |
Umap-learn (v0.5.1) |
Leland McInnes |
https://umap-learn.readthedocs.io/en/latest/ |
|
Other |
|
CPU (1 required) |
any core |
N/A |
RAM Memory |
N/A |
16 GB or greater recommended |
GPU |
NVIDIA GTX 1080Ti, 2080Ti or Titan RTX |
N/A |
OS |
Ubuntu v16.04, v18.04, or Windows 10 |
N/A |