The Problem

In correlative fluorescence and refractive index tomography, it is sometimes necessary to record phase and fluorescence images with different cameras, different frame rates, and different resolutions [SCG+17]. Handling these images and frame times easily gets out of hand (especially when they are stored in different files) and it would be nice to have a unified, data-driven interface to single fluorescence images and fluorescence series.

Why flimage?

There already exist many file formats for fluorescence data. I know that. However, I have made good experiences with the qpimage file format approach and wanted to have a similar API for the fluorescence data. This makes it easier to write transparent code for tomographic image analysis. Flimage also comes with a convenient bleach correction function.

Citing flimage

If you are using flimage in a scientific publication, please cite it with:

(...) using flimage version X.X.X (available at

or in a bibliography

Paul Müller (2017), flimage version X.X.X: Phase image analysis
[Software]. Available at

and replace X.X.X with the version of flimage that you used.