recipe cellprofiler

CellProfiler is free, open-source software for quantitative analysis of biological images.

Homepage:

https://github.com/CellProfiler/CellProfiler

Documentation:

https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.8/index.html

License:

BSD / BSD-3-Clause

Recipe:

/cellprofiler/meta.yaml

CellProfiler is free, open-source software for quantitative analysis of biological images.No prior experience in programming or computer vision is required.

package cellprofiler

versions:

4.2.8-0,  4.2.7-0,  4.2.6-0,  4.2.1-3,  4.2.1-2,  4.2.1-1,  4.2.1-0,  4.2.0-0,  3.1.9-1, 

4.2.8-0,  4.2.7-0,  4.2.6-0,  4.2.1-3,  4.2.1-2,  4.2.1-1,  4.2.1-0,  4.2.0-0,  3.1.9-1,  3.1.9-0

depends boto3:

>=1.12.28

depends cellprofiler-core:

4.2.8

depends centrosome:

depends docutils:

depends h5py:

>=3.6.0,<3.7.dev0,<4

depends imageio:

>=2.5

depends inflect:

depends jinja2:

depends joblib:

depends mahotas:

depends matplotlib-base:

depends mysqlclient:

depends numpy:

depends pillow:

depends prokaryote:

depends python:

>=3.8

depends python-bioformats:

depends python-javabridge:

depends pyzmq:

>=22.3,<23.dev0

depends requests:

depends scikit-image:

0.18.3

depends scikit-learn:

>=0.20,<1

depends scipy:

1.9.0

depends sentry-sdk:

depends six:

depends tifffile:

<2022.4.22

depends wxpython:

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 cellprofiler

and update with::

   mamba update cellprofiler

To create a new environment, run:

mamba create --name myenvname cellprofiler

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/cellprofiler:<tag>

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

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Link to this page

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