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plantseg-cellpose-augmentation

https://github.com/kreshuklab/plantseg-cellpose-augmentation

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (0.5%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: kreshuklab
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 12.5 MB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created over 4 years ago · Last pushed about 4 years ago
Metadata Files
Readme License Citation

README.md

Augmentation-in-3D-microscopy

Code for the master thesis

Owner

  • Name: kreshuklab
  • Login: kreshuklab
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Joel"
  given-names: "Ottosson"
  orcid: "https://orcid.org/0000-0003-0112-7575"
title: "Augmentation in 3D microscopy"
version: 1.0.0
doi: 10.5281/zenodo.1234
date-released: 2021-02-10
url: "https://github.com/AllaVinner/Augmentation-in-3D-microscopy/"

GitHub Events

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Dependencies

src/models/pytorch-3dunet/environment.yaml conda
  • h5py
  • hdbscan
  • matplotlib
  • pytest
  • python 3.8
  • pytorch
  • pyyaml
  • scikit-image
  • scikit-learn
  • scipy
  • tensorboardx
  • torchvision
src/models/cellpose/environment.yml pypi
  • PyQt5 *
  • PyQt5.sip *
  • cellpose *
  • google-cloud-storage *
  • natsort *
  • numba >=0.43.1
  • numpy >=1.20.0
  • opencv-python-headless *
  • pyqtgraph >=0.11.0rc0
  • scikit-image *
  • scikit-learn *
  • scipy *
  • tifffile *
  • torch >=1.6
  • tqdm *
src/models/cellpose/requirements.txt pypi
  • matplotlib *
  • mxnet *
  • natsort *
  • numba *
  • numpy *
  • pyqtgraph *
  • pytest *
  • scipy *
  • setuptools *
  • tifffile *
  • torch *
  • tqdm *