Biological image analysis (Fiji project)

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

Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., Haase, R., Jug, F. (2022) LABKIT: labeling and segmentation toolkit for big image data Frontiers in Computer Science 4, 777728

Haase R., Royer L.A., Steinbach P., Schmidt D., Dibrov A., Schmidt U., Weigert M., Maghelli N., Tomancak P., Jug F., Myers E.W. (2020) CLIJ: GPU-accelerated image processing for everyone Nature Methods, 17(1):5-6

Kožusznik J., Bainar P., Klímová J., Krumnikl M., Moravec P., Svatoň V., and Tomancak P. (2019) SPIM Workflow Manager for HPC Bioinformatics, btz140

Weigert M., Schmidt U., Boothe T., Müller A., Dibrov A., Jain A., Wilhelm B., Schmidt D.,  Broaddus C.,  Culley S.,  Rocha-Martins Segovia-Miranda F.,  Norden C.,  Henriques R.,  Zerial M.,  Solimena M.,  Rink J.,  Tomancak P.,  Royer R.,  Jug F.,  Myers E.W. (2018) Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy Nature Methods, 15(12):1090-1097

Pietzsch T., Preibisch S., Saalfeld S., Tomancak P. (2015) BigDataViewer: Interactive Visualization and Image Processing for Terabyte Data Sets Nature Methods 12, 481–483

Preibisch S., Amat F., Stamataki E., Sarov M., Myers E., Tomancak P. (2014) Efficient bayesian multi-view deconvolution Nature Methods, 7, 11(6):645-648

Pietszch T., Preibisch S., Tomancak P., Saalfeld S. (2012) Imglib2: Generic Image Processing in Java Bioinformatics 28(22): 3009-3011

Saalfeld S., Fetter R., Cardona A., Tomancak P. (2012) Elastic Volume Reconstruction from Series of Ultra-thin Microscopy Sections Nature Methods 9(7), 717-720

Cardona A., Saalfeld S., Schindelin J., Arganda-Carreras I., Preibisch S., Longair M., Tomancak P., Hartenstein V., Douglas R.J. (2012) TrakEM2 software for neural circuit reconstruction. PLoS ONE 7(6):38011

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., Schindelin J., Tomancak P. (2010) Software for bead-based registration of selective plane illumination microscopy data Nature Methods 7:418-419

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