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<!DOCTYPE html>
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What is the Image Processing Portal?
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The <a href="https://github.com/UQ-RCC/ipp" target="_blank">IPP</a> is a HTML based web interface for biologists to interact with High Performance Compute (HPC) systems at The University of Queensland.
The <a href="https://github.com/UQ-RCC/ipp" target="_blank">IPP</a> is designed and funded by the <a href="https://imb.uq.edu.au/microscopes" target="_blank">IMB Microscopy Facility</a> & the <a href="https://rcc.uq.edu.au" target="_blank"> Research Computing Centre (RCC)</a>
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Who can use the portal?
</h3>
Anyone with a UQ and Bunya account. A UQ-RDM needs to be mounted on the Bunya HPC to use with the portal. Click on the following <a href="https://uq-rcc.github.io/ipp-docs/#/access" target="_blank">link</a> to to learn more about setting up an account on the portal.
</div>
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Why a portal?
</h3>
<p>The <a href="https://github.com/UQ-RCC/ipp" target="_blank">IPP</a> makes using HPC resources possible by providing biologists with interactive tools in familiar and intuitive ways, by generating the required SLURM scripts and job submission documents automatically in the background without the need to know command-line!
</div>
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<h3 class="page-header">Features</h3>
<p>The IPP utilises the <a href="https://rcc.uq.edu.au/systems/high-performance-computing/bunya" target="_blank">Bunya</a> GPU-accelerated HPC system to make use of massively parallel image processing jobs.
The portal is backed by the <a href="https://rcc.uq.edu.au/systems/unstructured-data-collections" target="_blank">MeDiCI</a> network infrastructure and can access image data-sets mounted on the <a href="https://guides.library.uq.edu.au/research-and-teaching-staff/uq-research-data-manager" target="_blank">Research Data Manager (RDM)</a> GPFS based file system.</p>
<p>Currently the <a href="https://github.com/UQ-RCC/ipp" target="_blank">IPP</a> has the following pipelines enabled:<p/>
<div class="col-lg-12">
<li> <b>File Management</b>: The ability to explore, copy/paste, and delete files interactively from within the browser, allowing files to be moved between collections, or organised on native HPC infrastructure, without having to bring the files locally to the users device.</li>
<li> <b>Desktops Manager</b>: Allows to select an onBunya desktop, after which you'll be directed to a form where you can specify the resources required to launch the desktop </li>
<li> <b>Converter:</b> File conversion between the .ims (Imaris/Fusion) filetype and .tiff individual Z-stacks for accelerated ingest into Bunya. Coming soon .sld (Slidebook) will be implemented as a parallel processed for SButility (also developed by RCC).</li>
<li> <b>PreProcessing:</b> Batch processing and deskewing of Lattice Light-Sheet data-sets, as well as PSF distillation (bead centring & averaging).</li>
<li> <b>Deconvolution:</b> Currently utilising Microvolution Deconvolution (with Light-Sheet, Widefield, Confocal and 2-Photon modalities supported) for either individual files or directories of files. This mode also supports Generating a PSF or suppling your own measured PSF files. Deconvolution is currently supported on up to 10 nodes simultaneously utilising up to 40 GPUs.</li>
<li> <b>Job List:</b> Shows currently running jobs by the user by querying the SLURM queue</li>
</div>
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<div class="col-md-4" style="color:white; margin-top: 20px;font-size:14px">
<h5>Contacts </h5>
<hr />
<div>
<p>
<a href="https://imb.uq.edu.au/microscopy" target="_blank">IMB Microscopy</a><br />
<em>Project Lead & Design</em>
<div align="center">
<a href="mailto:microscopes@imb.uq.edu.au">microscopes@imb.uq.edu.au</a>
</div>
</p>
<p>
<a href="https://rcc.uq.edu.au/" target="_blank">Research Computing Center</a><br />
<em>Lead Developer</em>
<div align="center">
<a href="mailto:n.dasanayaka@uq.edu.au">n.dasanayaka@uq.edu.au</a>
</div>
</p>
<p>
<a href="https://qbi.uq.edu.au/research/facilities/information-technology-services" target="_blank">QBI IT Support</a><br />
<em>HPC Access and Support</em><br />
<div align="center">
<a href="mailto:helpdesk@qbi.uq.edu.au">helpdesk@qbi.uq.edu.au</a>
</div>
</p>
</div>
</div>
<div class="col-md-4" style="color:white; margin-top: 20px;font-size:14px">
<h5>Mailing address </h5>
<hr />
<div>
ACRF Cancer Biology Imaging Facility, <br />
Institute for Molecular Bioscience, <br />
level 6N, 306 Carmody Road, <br />
Building 80 <br />
University of Queensland, <br />
4072, St Lucia, <br />
Queensland, Australia
</div>
</div>
<div class="col-md-4" style="color:white; margin-top: 20px;font-size:14px">
<h5> Partners & support </h5>
<hr />
<div>
<p>
<a href="https://imb.uq.edu.au/microscopy">IMB Microscopy</a>
</p>
<p>
<a href="https://rcc.uq.edu.au/">UQ Research Computing Centre</a>
</p>
<p>
<a href="https://imb.uq.edu.au/profile/356/nicholas-condon">Dr Nicholas Condon</a> is supported by a Chan Zuckerberg Intitiative Fellowship
</p>
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