A napari plugin performing joint denoising and segmentation
of microscopy images using DenoiSeg.

View the Project on GitHub juglab/napari-denoiseg



If you do not have conda, we recommend installing miniconda or Anaconda.

  1. Then, in your command line tool create a conda environment
        conda create -n napari-denoiseg python=3.9
        conda activate napari-denoiseg
  2. Follow the TensorFlow installation step-by-step for your operating system.
  3. Install napari:
       pip install "napari[all]==0.4.15"
  4. Install napari-denoiseg:
       pip install napari-denoiseg


Note: These instructions are for GPU support. Apple’s tensorflow-metal is only officially supported for macOS 12 and higher. For CPU, you can try the Follow the TensorFlow instructions

  1. Set up env with napari and pyqt5
       conda create -n napari-denoiseg -c conda-forge python=3.9 napari pyqt5 imagecodecs
  2. Install tensorflow following Apple’s instructions
  3. Install napari-denoiseg
       pip install napari-denoiseg

Start napari-denoiseg

  1. Using the terminal with the napari-denoiseg environment active, start napari:

  2. Load one of the napari-denoiseg plugin.