recipe imctools

An Image Mass Cytometry (IMC) file conversion tool that aims to convert IMC rawfiles (.mcd, .txt) into an intermediary ome.tiff, containing all the relevant metadata. Further it contains tools to generate simpler tiff files that can be directly be used as input files for e.g. CellProfiller, Ilastik, Fiji etc

Homepage:

https://github.com/BodenmillerGroup/imctools

Documentation:

https://github.com/BodenmillerGroup/imctools/blob/master/README.md

License:

MIT

Recipe:

/imctools/meta.yaml

package imctools

(downloads) docker_imctools

versions:

2.1.8-0,  1.0.8-0,  1.0.7-0,  1.0.6-0,  1.0.5-0,  1.0.4-0,  1.0.3-0,  1.0.1-0,  0.2-0

depends numpy:

depends pandas:

depends python:

>=3.7

depends scikit-image:

depends scipy:

depends tifffile:

>=0.13.5

requirements:

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 imctools

and update with::

   mamba update imctools

To create a new environment, run:

mamba create --name myenvname imctools

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/imctools:<tag>

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

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Link to this page

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

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/imctools/README.html)