From 3c4e012411e75388dc50603839c6abf16c940d4a Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Wed, 23 Oct 2024 10:55:46 +0200 Subject: [PATCH] update readme --- README.md | 33 +++++++++++++-------------------- 1 file changed, 13 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index d2fdf99..0b90e21 100644 --- a/README.md +++ b/README.md @@ -1,26 +1,19 @@ -## Status - -A lot of the files and folders are in a early development state or may require -some serious refactoring. For now, I give a summary of the modules which are -somewhat stable already: - -| Module | Description | -| ----------------------------------- | --------------------------------------------------------------------------- | -| `depiction.spectrum` | Collection of spectra processing functionality. | -| `depiction.spectrum.baseline` | Estimate spectrum baseline curve. | -| `depiction.spectrum.peak_picking` | | -| `depiction.spectrum.peak_filtering` | | -| `depiction.calibration` | Calibration specific functionality. | -| `depiction.image` | Image specific functionality. | -| `depiction.parallel_ops` | Basic building blocks for parallelization of operations across \*ReadFiles. | -| `depiction.persistence` | Persistence specific code, including reader and writer for Imzml files. | -| `depiction.peak_filtering` | Peak filtering specific code. | -| `depiction.peak_picking` | Peak picking specific code. | -| `depiction.visualize` | Visualization specific code. | +# depiction + +This package provides functionality to process and visualize mass-spectrometry imaging data. +Currently, it requires your data to be available in the `imzML` format. +The full pipeline is also in the process of being developed. + +The project is structured in two general parts: + +- `depiction`: implements the whole functionality to process the data +- `depiction-targeted-preproc`: implements a pipeline that based on some configuration file creates outputs like qc report and .ome.tiff files + +This project is in an early state of development. If you are interested, it's best to reach out to us. ## Setup dev environment -### Using `uv` +### Using `uv` (recommended) Install the `pyproject.toml` in editable mode, tested with [uv](https://github.com/astral-sh/uv):