about
The bf-tools library is a set of routines that allows reading of various microscopy image formats directly into MATLAB. It is based on the LOCI Bio-Formats library and so should work with any format supported by that library. However, I have only tested it with Leica LIF files and Bitplane Imaris 5.5 files.
I put this together because, while there are a couple of other MATLAB interfaces for the library, there didn’t seem to be one that was simple and lightweight while also giving granular access to the data. This was a problem for me since our datasets tend to get obnoxiously large so trying to load the whole thing was futile. I suspect we are not alone in this regard.
While there are many things that can be added and improved, the library seems to be usable so I figured it would be good thing to share.
The latest stable release can be downloaded here . All revisions and releases are also available on github. Feel free to fork away.
Setup is incredibly simple. The routines take care of a some annoying parts.
- Download the latest release from the link above
- Uncompress the archive
- Add the resulting folder to your MATLAB path
bf-tools is released under a BSD license, so anyone can do pretty much anything with it. Bio-formats is released under the GPL. I have put a copy of the binary within this source tree for convenience but that may not be entirely kosher. If I have to remove the jar, it just means that there will be a couple of extra setup steps.