saeyslab/cifconvert

cifconvert is a package built on the python-bioformats package that saves images and masks from the proprietary Amnis CIF-file format to an HDF5 file.

This package has been deprecated. Please use ifcimglib

cifconvert

cifconvert is a package built on the python-bioformats package that saves images and masks from the proprietary Amnis CIF-file format to an HDF5 file.

Installation

Requirements

Python

Install

Clone this repository:

git clone https://github.com/saeyslab

Install dependencies using the pip package manager:

pip install -r requirements.txt

Usage

This package has two functions:

• cifconvert for converting CIF-files to HDF5-files,
• and cifmerge for creating Virtual HDF5 Datasets from existing HDF5-files.

cifconvert

usage: cifconvert [-h] [--channels [CHANNELS [CHANNELS ...]]] [--debug]
                  cif output width height

positional arguments:
  cif                   Input cif containing images.
  output                Output filename for h5.
  width                 Width to crop or padd images to.
  height                Height to crop or pad images to.

optional arguments:
  -h, --help            show this help message and exit
  --channels [CHANNELS [CHANNELS ...]], -c [CHANNELS [CHANNELS ...]]
                        Images from these channels will be extracted. Default
                        is to extract all.
  --debug               Show debugging information.

cifmerge

usage: cifconvert [-h] output [h5s [h5s ...]]

positional arguments:
  output      Output filename for h5.
  h5s         h5 datasets to concatenate in virtual dataset.

optional arguments:
  -h, --help  show this help message and exit