- recipe unetcoreograph
UNetCoreograph - Automated segmentation of nuclei in 3D imaging data.
- Homepage:
- License:
MIT / MIT
- Recipe:
UNetCoreograph is a Python tool for segmenting and analyzing nuclei in tissue images using a U-Net based model.
- package unetcoreograph¶
- Versions:
2.4.6-0,2.4.5-0,2.4.4-0,2.4.3-0- Depends:
on h5py
on matplotlib-base
on numpy
on pandas
on python
>=3.7on scikit-image
on scipy
on tifffile
on tqdm
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install unetcoreograph
to add into an existing workspace instead, run:
pixi add unetcoreograph
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install unetcoreograph
Alternatively, to install into a new environment, run:
conda create -n envname unetcoreograph
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/unetcoreograph:<tag>
(see unetcoreograph/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/unetcoreograph/README.html)
