recipe unetcoreograph

UNetCoreograph - Automated segmentation of nuclei in 3D imaging data.

Homepage:

https://github.com/HMS-IDAC/UNetCoreograph

License:

MIT / MIT

Recipe:

/unetcoreograph/meta.yaml

UNetCoreograph is a Python tool for segmenting and analyzing nuclei in tissue images using a U-Net based model.

package unetcoreograph

(downloads) docker_unetcoreograph

versions:

2.4.4-0,  2.4.3-0

depends h5py:

depends matplotlib-base:

depends numpy:

depends pandas:

depends python:

>=3.7

depends scikit-image:

depends scipy:

depends tifffile:

depends tqdm:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install unetcoreograph

and update with::

   mamba update unetcoreograph

To create a new environment, run:

mamba create --name myenvname unetcoreograph

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/unetcoreograph:<tag>

(see `unetcoreograph/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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