Chromagnon

Image correction software for chromatic shifts in fluorescence microscopy.

Acceptable image file formats

Reading

• Most microscopy formats (same as ImageJ)

Writing

• multipage-tiff (imageJ format or ome.tif format)
• DeltaVision (.dv)

How it works

Read the document.

If you prefer, watch the movie by JoVE.

The full text article describes in more detail about sample preparation, software usage, trouble shooting, etc...

Downloads

The ready to use packages are available here

Example Images

Example images for testing are available (422 MB)

The source

The source code is written in pure python and works on the following platforms and dependencies.

Platforms successfully tested:

• MacOSX64bit (10.9.5 or higher)
• Windows64bit (XP or higher)
• Linux Ubuntu(16-18), CentOS(6)

Dependencies:

• python (v2.7 or >v3.6)
• numpy
• scipy
• chardet (optional for GUI)
• wxPython (optional for GUI)
• PyOpenGL (optional for GUI)
• pyFFTW (optional for fast Fourier transform)
• tifffile <= 2021.7.2 (optional for reading/writing tiff)
• nd2 (optional for reading Nikon nd2 file)
• javabridge (optional for reading more image file formats)
• python-bioformats (optional for reading more image file formats)
• lxml (optional for reading more image file formats)
• Java Development Kit (optional for reading more image file formats)

How to cite

Please cite our paper:

1. Matsuda, Schermelleh, Hirano, Haraguchi, Hiraoka, 2018 "Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy" Sci Rep 8:7583

2. Matsuda, Kojin, Schermelleh, Haraguchi, Hiraoka, 2020 "High-Accuracy Correction of 3D Chromatic Shifts in the Age of Super-Resolution Biological Imaging Using Chromagnon." J. Vis. Exp. (160), e60800

Authored and maintained by Atsushi Matsuda.