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. 2022 Jun 14;3(3):101469. doi: 10.1016/j.xpro.2022.101469
REAGENT or RESOURCE SOURCE IDENTIFIER
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