Research Groups

Biological image analysis (Fiji project)

Example of 3d stitching of tiled confocal acquisition of the Drosophila larval nervous system

Stephan Saalfeld, Stephan Preibisch, Tobias Pietzsch

In order to extract computationally tractable gene expression information from large 3D and 4D recordings of embryos, we need to employ advanced 3D image analysis and computer vision approaches such as rigid and elastic specimen-to-specimen or specimen-to-atlas registration, segmentation, object recognition and motion tracking (Eliceiri et al. 2012).

Thus far we developed state-of-the-art approaches to stitching of confocal microscopy data (nD) (Preibisch et al. 2009), registration of massive electron microscopy datasets and various approaches for registration of multi-view microscopy datasets, in particular from SPIM.

We collect our advances under the umbrella of the Fiji (Fiji Is Just ImageJ) which is an open source project build around popular biological image analysis platform ImageJ (Schindelin et al. 2012). Through Fiji we established a community of researchers interested in combining biology and image analysis (Cardona and Tomancak 2012). We aim to create usable, thoroughly documented tools for the whole biology community. Recognizing the fact that Fiji cannot possibly adequately cover all the diversity of applications in biological image analysis we try to actively build bridges to other open source bioimage informatics platforms. We work particularly closely with ImageJ2 project, but have established contacts (through regularly organized hackathons) to BioFormats, OME, CellProfiler, ITK, KNIME, Icy, microManager and more. Our programmers developed ImgLib2, a library for generic image processing in Java, which will serve as common approach for image data representation enhancing the interoperability of the open source bioimage projects (SciJava).

collaborators:  Johannes Schindelin & Kevin Eliceiri (LOCI Madison), Albert Cardona and the Fiji open source community

funding: Believe it or not but NONE! We acknowledge the generous support of MPI-CBG, HFSP and ERC that keeps the project alive.

Related Publications

Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Preibisch S., Rueden C., Saalfeld S., Schmid B., Tinevez J., Hartenstein V., Eliceiri K., Tomancak P., Cardona A. (2012) Fiji - an open source platform for biological image Nature Methods 9(7), 676-682

Eliceiri K. V., Berthold M. R., Goldberg I. G., Ibanez L., Manjunath B. S., Martone M. E., Murphy R. F., Peng H., Plant A. L., Roysam B., Stuurmann N., Swedlow J.R., Tomancak P., Carpenter A. E. (2012) Biological Imaging Software Tools Nature Methods 9(7), 697-710

Cardona A., Tomancak P. (2012) Current challenges in open-source bioimage informatics Nature Methods 9(7), 661-665

Preibisch S., Saalfeld S., Tomancak P. (2009) Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics Jun 1;25(11):1463-5