BioFormats Image Toolbox

Most commercial microscopes use proprietary formats to save imaging data (e.g. Nikon uses ND2, Leica uses LZI). These formats cannot be read by standard methods, such as MATLAB’s imread function. To overcome this issue, the OME Consortium developed a Java library that is able to read these formats, returning image data as a standard array that can be manipulated in MATLAB.

This toolbox was written to implement a MATLAB class BioformatsImage that wraps around this library. My goal was to develop an easy-to-use interface with the library, providing access to both image data and metadata from the experiment. The toolbox also automatically downloads the OME library if it is not detected on the current system.


Code, compiled MATLAB toolboxes, and instructions can be found here.

Note: A different approach to read Nikon’s ND2 files natively using the official SDK is also available.


A huge thank you to the OME Consortium for providing the original Java library.