Johannes Schindelin

Microsoft

Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, and heterogeneity of image datasets but also in the tooling used to analyze this data. This wealth of image analysis tools, spanning different programming languages, frameworks, and data structures, is itself a problem for dat...

Many scientific software platforms provide plugin mechanisms that simplify the integration, deployment, and execution of externally developed functionality. One of the most widely used platforms in the imaging space is Fiji, a popular open-source application for scientific image analysis. Fiji incorporates and builds on the ImageJ and ImageJ2 platf...

Background ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulte...

State-of-the-art light and electron microscopes are capable of acquiring large image datasets, but quantitatively evaluating the data often involves manually annotating structures of interest. This processis time-consuming and often a major bottleneck in the evaluation pipeline. To overcome this problem, we have introduced the Trainable Weka Segmen...

We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over ti...

To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain. Participants submitted boundary maps predicted for a test set of images, and were scored based on their agreement with a consensus of human expert annotations....

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a...

Unlabelled: Murine cells exhibit a profound block to HIV-1 virion production that was recently mapped to a species-specific structural attribute of the murine version of the chromosomal region maintenance 1 (mCRM1) nuclear export receptor and rescued by the expression of human CRM1 (hCRM1). In human cells, the HIV-1 Rev protein recruits hCRM1 to i...

Collection of ImageJ code to address bleaching

During embryonic development, temporal and spatial cues are coordinated to generate a segmented body axis. In sequentially segmenting animals, the rhythm of segmentation is reported to be controlled by the time scale of genetic oscillations that periodically trigger new segment formation. However, we present real-time measurements of genetic oscill...

Segmentation is a periodic and sequential morphogenetic process in vertebrates. This rhythmic formation of blocks of tissue called somites along the body axis is evidence of a genetic oscillator patterning the developing embryo. In zebrafish, the intracellular clock driving segmentation is comprised of members of the Her/Hes transcription factor fa...

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.

Light sheet microscopy promises to revolutionize developmental biology by enabling live in toto imaging of entire embryos with minimal phototoxicity. We present a open hardware and software platform for constructing a compact and customizable Selective Plane Illumination Microscope (SPIM). The OpenSPIM platform including detailed instructions is sh...

Light sheet microscopy promises to revolutionize developmental biology by enabling live in toto imaging of entire embryos with minimal phototoxicity. We present detailed instructions for building a compact and customizable Selective Plane Illumination Microscopy (SPIM) system. The integrated OpenSPIM hardware and software platform is shared with th...

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms int...

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruct...

Correctable noise on EM images. A1, A2 A large blob occludes information on an EM image when the display range is adjusted for the whole image (A1), but reveals its content when CLAHE is applied (A2). B1-4 A support-film fold generates a dark band (B1) whose content is discernible at a lower value region of the histogram (inset in B2). Applying CLA...

On-the-fly processing of the field of view for enhanced contrast. The live filter tab of the display offers a few filters, to adjust A the display range; invert the image (not shown) or B CLAHE. Yellow rectangle indicates the original view without filters. (PDF)

Sketching and quantifying neural tissue with spheres and tubes. A,B Two sections with a “ball” to represent the nucleus and a “pipe” to model the main process of a monopolar insect neuron. The colors indicate relative depth: red means below the current section and blue above. C 3d representation of the “ball” and “pipe” traversing multiple sections...

Measurements. A Example of a “connector” instance, expressing a synapse between an axon (large profile at lower left with numerous microtubules) whose tree is tagged “presynaptic site”, with numerous terminal dendrites (small target circles, one in red indicating it’s in the previous section). B Measurement of the distances from the root node (the...

Expressing image transformations without duplicating the original images by using alpha masks. Duplicating images has a huge cost in data storage which TrakEM2 avoids by using highly compressible alpha masks and precomputed mipmaps stored with lossy compression. A Images present borders which are apparent when overlapping (red arrowheads). An alpha...

Volumetric reconstruction with series of complex 2d areas or “area lists”. The “Z space” tab lists all segmentation objects that exist in 3d. A With the brush tool, a selected “area list” instance is painted in yellow (notice the mouse pointer with circle), labeling the sectioned profile of a neuron. The selected object (listed in the cyan panel) m...

Supplemental Text containing detailed information on various aspects of the TrakEM2 software, including image registration, dealing with noise, alpha masks, manual segmentation with areas, balls and pipe objects, and measurements. (PDF)

Manual non-linear transform of collections of image tiles for fine cross-section alignment. A,B Two consecutive sections numbered 344 and 345 present an artefactual stretch, as indicated by the widening of the marked profiles (in white). C,D The manual non-linear transformation mode is used here in conjunction with the transparent section overlay (...

The Drosophila brain is formed by an invariant set of lineages, each of which is derived from a unique neural stem cell (neuroblast) and forms a genetic and structural unit of the brain. The task of reconstructing brain circuitry at the level of individual neurons can be made significantly easier by assigning neurons to their respective lineages. I...

The core contribution of this paper is an elegant and robust method to match and register partially overlapping rotated subsets of random 3D point clouds. We identify corresponding points by matching the local configuration of spatial nearest neighbors invariantly to translation, rotation and optionally scale. This set of correspondence candidates...

Direct volume editing. A movie which shows the result of the simulated dendritic growth. The corresponding source code is presented in Additional file 1, section 2.

Supplementary material. Top, demonstration of landmark selection in two different adult Drosophila brains, for the purpose of landmark-based image volume registration. Bottom, source code example implementing the dendritic growth simulation shown in Figure 4 of the main manuscript.

Software. The JAR archive, containing both binary classes and the Java source code of our software. To install the software, this file must be copied into ImageJ's plugins directory.

Basic usage. A movie which demonstrates the basic usage of the ImageJ plugin provided by our framework. More screen casts are available on our web page.

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D re...

The peristimulus time histogram (PSTH) and the spike density function (SDF) are commonly used in the analysis of neurophysiological data. The PSTH is usually obtained by binning spike trains, the SDF being a (Gaussian) kernel smoothed version of the PSTH. While selection of the bin width or kernel size is often relatively arbitrary there have been...

The peristimulus time histogram (PSTH) and its more continuous cousin, the spike density function (SDF) are staples in the analytic toolkit of neurophysiol- ogists. The former is usually obtained by binning spike trains, whereas the stan- dard method for the latter is smoothing with a Gaussian kernel. Selection of a bin width or a kernel size is of...

Method The peristimulus time histogram (PSTH) and its more continuous cousin, the spike density function (SDF) are staples in the analytic tool kit of neurophysiologists. The former is usually obtained by binning spike trains, whereas the standard method for the latter is smoothing with a Gaussian kernel. Selection of a bin width or a kernel size i...

In the fly Drosophila melanogaster, new genetic, physiological, molecular and behavioral techniques for the functional analysis of the brain are rapidly accumulating. These diverse investigations on the function of the insect brain use gene expression patterns that can be visualized and provide the means for manipulating groups of neurons as a comm...

In this thesis, I introduce the Virtual Brain Protocol, which facilitates applications of the Standard Brain of Drosophila melanogaster. By providing reliable and extensible tools for the handling of neuroanatomical data, this protocol simplifies and organizes the recurring tasks involved in these applications. It is demonstrated that this protocol...

We introduce a metric for probability distributions, which is bounded, information-theoretically motivated, and has a natural Bayesian interpretation. The square root of the well-known χ² distance is an asymptotic approximation to it. Moreover, it is a close relative of the capacitory discrimination and Jensen-Shannon divergence.