Tools

Illoura

Illoura is a key piece of software in the project. It provides scientists with a 3D environment in which they can freely roam about inside an actual (reconstructed) biological cell. The 3D objects are organised in the visualiser using an ontology, allowing users to associate attributes found in the various external bioinformatics databases to cellular objects, perform queries against multiple datasets, infer semantic relationships, and have the results consolidated in the Visible Cell® environment in a meaningful way. It can be thought of as the interface to an interactive atlas for cellular data.

Illoura grew out of ideas and work initiated between the groups of Associate Professor Ben Hankamer and Dr Brad Marsh at the IMB, specifically Igor Kromin's prototype visualisation software which formed part of his information technology (ITEE) honours degree thesis. The production software - based on this prototype - has been extensively developed by the Visible Cell® project staff in close collaboration with the group of Dr Brad Marsh.

iCluster

iCluster is a complete integrated methodology we have developed for testing for difference in fluorescent protein subcellular localisation imaging. iCluster combines components for automated statistics generation, spatial organisation and layout of image sets by similarity to enable patterns of difference in image sets to be seen and browsed, and statistical testing to give rigorous confirmation of differences between experiments.

OBCOL

OBCOL is software we designed to perform organelle-based colocalisation analysis from multi-fluorophore microscopy 2D, 3D and 4D cell imaging. It is implemented as an ImageJ plugin, and source code is included in the distribution jar file.

Cell Centered Database

Cell Centered Database (CCDB) is being developed by the U.S. National Center for Microscopy and Imaging Research (NCMIR) to store 3D light and electron microscsope reconstructions of cells.

Cell Visualiser uses a CCDB installation at the IMB for its data repository. In colabaration with NCIMR, work is currently underway to extend CCDB to better serve the requirements of the Cell Visualiser. These extensions will later be incorporated into CCDB.

Cell Illustrator

Cell Illustrator, developed at the Human Genome Centre, Univerity of Tokyo and Yamaguchi University, is a tool that models regulatory networks. It uses 2D schematic models of the pathway network. It is a goal of the Visible Cell® project to map the output of Cell Illustrator (or other similar tools) onto a 3D physical model of the cell so that network models can be integrated and visualised into the Cell Visualiser environment.

Sequence Retrieval System

SRS is a middleware layer that enables queries accross diverse sequence databanks. The results of these queries can then be combined with local data and the results displayed in a graphical format when appropriate. SRS is a product from biowisdom and has been made available to the project via the Queensland Facility for Advanced Bioinformatics (QFAB).

SwarmPS

SwarmPS is a software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms and an extensive set of tools. These include multiple image handling (~10²), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible and fast and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

DomainDraw

DomainDraw is software for creating schematic diagrams of protein domains or motifs. Multiple protein domain architectures may be aligned and visualised simultaneously.  Currently it is being used for domain visualisation within the LOCATE subcellular localisation database. DomainDraw is available via a web interface or as executable software on request.

DBL Filter

Advances in 3D electron microscopy (EM) and image processing are providing considerable improvements in the resolution of subcellular volumes, macromolecular assemblies and individual proteins. However, the recovery of high-frequency information from biological samples is hindered by specimen sensitivity to beam damage. Low-dose electron cryo-microscopy conditions afford reduced beam damage but typically yield images with reduced contrast and low signal-to-noise ratios (SNRs). The new discriminative bilateral (DBL) filter is based upon the bilateral filter implementation of Jiang et al., (2003). In contrast to the latter, the DBL filter can distinguish between object edges and high-frequency noise pixels through the use of an additional photometric exclusion function. As a result, high-frequency noise pixels are smoothed, yet object edge detail is preserved. In the present study we show that the DBL filter effectively reduces noise in low SNR single particle data as well as cellular tomograms of stained plastic sections.

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