Installation instructions¶

Installation¶

imaging+ can be installed by downloading or cloning the GitHub repository and running:

python

pip install -e imagingplus

on the command line from the directory where the GitHub repository was downloaded to.

Note: The package is installable as a stand-alone python package. You can install the package into an existing conda environment, or you may choose to skip using conda environment all together.

To setup in a conda environment, we recommend following the steps below (on the command line):

Clone the GitHub repository using Git:

default

git clone https://github.com/Packer-Lab/imagingplus.git

Create a new conda environment using the plitest.yml provided in this repository by running:
default
```
conda env create -f plitest.yml
```
Activate the conda environment:
default
```
conda activate plitest
```
cd to the parent directory of where this repo was downloaded to.

From this parent directly, run:

default

pip install -e imagingplus

# this installs the package under developer settings (preferred for current release).

Test/Import Installation¶

Test imaging+ is successfully installed by importing the package in python:

Ensure that the conda environment from which imaging+ was installed is activated.
start python on the command line using:
default
```
python
```

or start a python session from the same conda environment in your preferred method (e.g. jupyter notebook or IDE).

Import the package:

default

import imagingplus
# or
import imagingplus as ip

– Ignore any warnings or printed messages :) –

Dependencies¶

imaging+ requires the use of multiple scientific python packages (e.g numpy, pandas, anndata, matplotlib). These dependencies should be automatically installed as required when installing imaging+. It is common to have conflicts with dependencies that might require manually uninstalling and re-installing specified versions. However, if there are non-trivial issues with dependencies during installation, please report this by raising an issue on Github.

Next¶

Core structures

Quick Start Guide