i2nca

i2nca is a Mass Spectrometry Imaging INteractive Conversion and Quality Assesment tool bundle. It is desinged to utilize the powerful file reading capabilities of m2aia and provide a workflow package. The current workflows allow for MSI data preprocessing in the .imzml data format.

Installation:

i2nca is distributed through a number of channels. The builds of i2nca are plattform-independent and testes on Linux and Windows.

Install it with pip via:

pip install i2nca

or via the bioconda channel

currently on the way

or for dev use, install the provided conda recipe and use the pip+github install

conda env create -n env_name -f path\to\file\...\conda_recipe.yml
conda activate env_name
pip install i2nca@git+https://github.com/cKNUSPeR/i2nca.git

Update from github via:

pip uninstall i2nca
pip install i2nca@git+https://github.com/cKNUSPeR/i2nca.git

Brukertools

i2nca features tools that access the Bruker propietary formats for MSI data (.tsf and .tdf). These need the additional TDF-SKD distributed by Bruker. To install these tools, follow these steps:

1. Get the TDF-SKD from Bruker (distributed for free at Bruker)
2. Install i2nca into a virtual env (like a conda env)
3. Copy the files timsdata.dll and timsdata.lib from the TDF-SDK and place them at the level of the python executable of the env.
4. Reinstall i2nca into the env with the following command

pip uninstall i2nca
pip install i2nca@git+https://github.com/cKNUSPeR/i2nca.git@brukertools