3D visualisation of the distribution of the phylum Chytridomycota (zoosporic fungi) dataset

Full description

The phylum Chytridiomycota (chytrid) is an ancient group of zoosporic fungi. The dataset relates to a project led by Dr Osu Lilje, Dr Frank Gleason and Dr Peter McGee of the University of Sydney, that aims to investigate the way that chytrids may be involved in the restructuring of soil particles, and the long-term storage and sequestration of carbon in soil.

The dataset relates specifically to the development of a new technique using computer aided tomography to visualise and quantify the distribution of fungi in three dimensions. The technique utilises the MicroCT imaging facilities at the Australian Centre for Microscopy and Microanalysis (ACMM) at the University of Sydney.  The technique has been developed and documented by Dr Lilje, and is being tested under varying conditions through a suite of PhD projects.

The dataset consists of TIFF and BMP files, documented lab protocols, instrument calibration and process documentation in various formats, and handwritten documentation of each sample and treatment in lab notebooks.  Chytrid samples are imaged using a Skyscan 1072 Micro-Computed Tomography (MicroCT) scanner, creating a raw dataset of high-resolution .TIFF files averaging 2GB each in size.  NRecon software is then used to convert the native TIFF files to bitmap format (.bmp). The bitmap image files are then imported into VGStudioMax, and CTAnalyser software.  VGStudioMax matches grayscale values identified in the 2D bitmap files to generate a 3D visualisation of the image data, and CTAnalyser uses grayscale values to generate a quantitative measurement of the distribution of chytrids through a particle matrix.