README.Rmd

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![Image](./im/cciaLogo.png)

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The goal of `cecelia` is to simplify image analysis for immunologists and integrate
static and live cell imaging with flow cytometry data. The package primarily builds upon
[`napari`](https://napari.org) and [`shiny`](https://shiny.rstudio.com/). Our aim was 
to combine shiny's graph plotting engine with napari's image display.

__This package is pre-alpha__

# Genereal installation guidelines

## System requirements

Software dependencies will be installed during the installation processing of the R-package.
The framework has primarily been tested on an old MacOS 12.7.6 (with HPC access) and new M2 14.6.1.
To install the software on Windows PCs you must install the [`Docker`](https://github.com/schienstockd/ceceliaDocker) version.
For cell segmentation and deep learning denoising we recommend a GPU that is recognised by [`torch`](https://pytorch.org/get-started/locally/).

## Installation guide

See [`read-the-docs`](https://cecelia.readthedocs.io/en/latest/index.html) for installation and tutorials.
Installation of the R-package with all shiny and python dependencies should require less than 1 h.
The Docker based installation depends on the user's bandwidth but typically requires less than 20 min.