This repository contains scripts and the relative workflow for the conversion of .cif file into multichannel .ome.tiff images which are redable by BioFormats. The workflow includes the injection of an ome.xml into the tiff header. The images will be readen in OMERO with the correspective channels. Furthermore, the script include the extraction on mask and their upload into OMERO as ROIs.
The JN include the complete workflow with upload into OMERO using the package ezomero.
- Extraction of single channels and metadata from the .cif is performed with R using the package IFC. Please check the corrispetively repository for more info the IFC usage
- Creation of the multichannel images and mask upload is performed with python >= 3.8
The script was tested with the following packages
R:
- R == 4.1.2
- IFC == 0.2.1.500
- jsonlite == 1.8.8
Python:
- Create a multichannel image:
- python >= 3.8
- scikit-image == 0.21.0
- ome_types == 0.5.1post1
- tifffile == 2023.7.10
- Mask and image import:
- ezomero == 3.0.0
- omero-rois == 0.3.0
IMPORTANT!!! PLEASE READ THE IFC PACKAGE DISCLAIMER BEFORE RUNNING THE SCRIPT!!!
The multichannel creation can be potentially run also over R. Please check the GitHub issue gitdemont/IFC#5