Zerial Lab - Resources

Protocols

Early Endosome Fusion Assay

With this in vitro assay we queried the necessary components for endosomal fusion in Ohya et al. (2009).

Primary Mouse Hepatocyte Isolation

We use this protocol published in Zeigerer et al. (2017) to isolate primary hepatocytes from mouse livers for sandwich cell culture.

Plating of Isolated Primary Hepatocytes

This protocol describes in detail how we plate freshly isolated primary mouse hepatocytes for collagen sandwich culture. We published it in Zeigerer et al. (2012).

Fluorescence Immunostaining with Clearing for 3D Reconstruction

Here we describe how we clear and stain thick tissue sections for digital 3D tissue reconstruction. The method was published in Morales-Navarrete et al., eLife (2019).

Staining Protocol for Hepatocytes in Collagen Sandwich Culture

We use this method published in Zeigerer et al. (2017) for antibody staining of samples for immunofluorescence microscopy.

Endosomics

The Endosomics database gives you the possibility to query your gene of interest´s phenotype in endocytosis upon siRNA knockdown. This database is the product of Collinet et al. (2010), where we profiled the human genome relative to a set of 58 parameters that quantitatively describe endocytic features.

In this study, we queried between 3 to 8 different siRNAs per gene and analyzed more than 50 parameters in the cell to describe the obtained phenotype. From this survey, we attributed new functions to known and unknown genes with respect to EGF- and transferrin-mediated endocytosis.

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MotionTracking Software

MotionTracking can extract more than 100 different statistical parameters from microscopy data.

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Manuals

MotionTracking is a collection of visualization, processing and image analysis tools. We started the project in 2001 to track the movement of intracellular vesicles and later expanded it to high-performance calculations of high-throughput genome-wide screening data and liver tissue 3D analysis. We build MotionTracking as a language-stack paradigm, where semantically different parts of applications are implemented based on different programming languages:

The general logic flow of data processing, algorithms, and user interface in the dynamic object-oriented language Pluk, number crunching algorithms in C++ and OpenCL, and the interface of the operating system GUI and object-oriented database access in specialized declarative languages (OWML and ODML).

This approach automates code generation and accelerates the prototyping and logic design of algorithms. Thus, MotionTracking can extract more than 100 different statistical parameters from microscopy data.

Pleomorphic object detection with a size range from the diffraction limit to few a micrometres

Tracking of intracellular objects in timelapse data

Object-oriented marker co-localization analysis

Active Mesh based analysis and quantification in 3D

Segmentation and reconstruction of nuclei, cell and tubular networks segmentation in 2D or 3D volumes

Powerful statistical analysis tools