imctools

An IMC file conversion tool that aims to convert IMC raw data files (.mcd, .txt) into an intermediary ome.tiff, containing all the relevant metadata. Further it contains tools to generate simpler TIFF files that can be directly be used as input files for e.g. CellProfiller, Ilastik, Fiji etc.

Documentation is available at https://bodenmillergroup.github.io/imctools

Requirements

This package requires Python 3.7 or later.

Using virtual environments is strongly recommended.

Installation

Install imctools and its dependencies with:

pip install imctools

Usage

See Quickstart

Authors

Created and maintained by Vito Zanotelli vito.zanotelli@uzh.ch and Anton Rau anton.rau@uzh.ch

Contributing

Contributing

Changelog

Changelog

License

MIT

• Quickstart
  • Features
  • Prerequisites
  • Installation
  • Usage of version 2.x
  • Usage of version 1.x
• API reference
  • imctools.cli
  • imctools.converters
  • imctools.data
    • imctools.data.acquisition
    • imctools.data.acquisitiondata
    • imctools.data.channel
    • imctools.data.panorama
    • imctools.data.session
    • imctools.data.slide
  • imctools.io
    • imctools.io.utils
    • imctools.io.imc
    • imctools.io.mcd
    • imctools.io.ometiff
    • imctools.io.txt
• Contributing
• Changelog
  • [2.1.8] - 2021-09-12
  • [2.1.7] - 2021-05-21
  • [2.1.6] - 2021-03-16
  • [2.1.5] - 2021-03-03
  • [2.1.4] - 2021-02-01
  • [2.1.3] - 2021-01-21
  • [2.1.2] - 2021-01-21
  • [2.1.1] - 2021-01-20
  • [2.0.1] - 2020-08-14
  • [2.0.0] - 2020-08-12
• License