https://github.com/jni/cellom2tif

Python command line interface to convert Cellomics .C01 files to TIFF.
https://github.com/jni/cellom2tif

Last synced: about 1 month ago
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Python command line interface to convert Cellomics .C01 files to TIFF.

• Host: GitHub
• URL: https://github.com/jni/cellom2tif
• Owner: jni
• License: bsd-3-clause
• Created: 2013-06-04T15:01:36.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2019-03-10T02:42:52.000Z (over 5 years ago)
• Last Synced: 2024-10-05T00:30:56.102Z (about 2 months ago)
• Language: Python
• Homepage:
• Size: 20 MB
• Stars: 2
• Watchers: 4
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
cellom2tif

==========

Python script to convert Cellomics files to TIFF.

Read the BioFormats [report card for Cellomics

files](https://www.openmicroscopy.org/site/support/bio-formats5/formats/cellomics.html).

In short: it's not a great format. So you might as well convert all your

Cellomics files to TIFF and forget about them forever. Software developers

will thank you.

# Continuous integration

Cellom2tif uses Travis-CI and Coveralls for continuous integration:

[![Build Status](https://travis-ci.org/jni/cellom2tif.svg?branch=master)](https://travis-ci.org/jni/cellom2tif)

[![Coverage Status](https://img.shields.io/coveralls/jni/cellom2tif.svg)](https://coveralls.io/r/jni/cellom2tif)

# Dependencies

Uses [python-bioformats](http://pythonhosted.org/python-bioformats) and

[javabridge](http://pythonhosted.org/javabridge) to perform the conversion.

- numpy >= 1.6

- javabridge >= 1.0.3

- python-bioformats >= 1.0.3

Note that (much of) Python BioFormats is GPL-licensed (v2). All the code

in cellom2tif is BSD-licensed (3-clause), *except where it is forbidden by the

GPL* by the import of Python BioFormats.  Consult your lawyer.

(I don't have one.)

# Usage

```

$ cellom2tif -h

usage: cellom2tif [-h] [-E FILENAME] [-m] [-v] root_path out_path

Convert a bunch of Cellomics files to TIFFs. Currently supports the .CO1 and 

.DIB format.

positional arguments:

  root_path             The path containing the Cellomics files

  out_path              The path to output the TIFFs.

optional arguments:

  -h, --help            show this help message and exit

  -E FILENAME, --error-file FILENAME

                        Log problem filenames to the given filename.

  -m, --ignore-masks    Ignore files ending in "o1".

  -v, --verbose         Print out runtime information.

```

Note that weird behavior may occur when the input and output directories are

the same, or subdirectories of one another, since the script recurses down

subdirectories and recreates the subdirectory structure in the output path.

# Licenses

Christoph Gohlke's excellent

[tifffile.py](http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html) is included

for easy writing of TIFF files, and is itself BSD-licensed (3-clause).

As noted above (Dependencies), cellom2tif is BSD-licensed (where possible), and

GPLv2-licensed (where required).

# Author

Juan Nunez-Iglesias ([email protected]).