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UQ-RCC / ipp

The IPP is a Web portal for biologists to interact with High Performance Compute (HPC) systems. Designed and funded by the IMB Microscopy Facility & the Research Computing Centre (RCC)
https://rcc.uq.edu.au/
MIT License
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Open source deconvolution engine #52

Open DrSpringy opened 2 years ago

DrSpringy commented 2 years ago

We need to provide an alternative open source deconvolution option for places that don’t have access to microvolution It could possibly use the same deconvolution GUI we have now, but allow the user to select which deconvolution engine to use? This would need to be done before setting deconvolution parameters as some microvolution features may be disabled such as

  https://github.com/scopetools/cudaDecon   https://github.com/tlambert03/pycudadecon   https://www.sciencedirect.com/science/article/pii/S1046202316305096   https://www.researchgate.net/publication/312099578_DeconvolutionLab2_An_Open-Source_Software_for_Deconvolution_Microscopy   https://www.degruyter.com/document/doi/10.1515/bams-2020-0027/html

NickCondon commented 2 years ago

https://github.com/clEsperanto/pyclesperanto_prototype/blob/master/demo/transforms/deskew.ipynb

Deskew by Robert Haase

DrSpringy commented 7 months ago

has this been thoroughly tested?

markendr commented 5 months ago

JS, NC, ND, ME zoom call on 20-Mar-2024:

Nick/James to test cudadecon, open CRM ticket if bugs found

Update to allow users to select from available decon tools: eg. Microvolution, cudadecon, Huygens, and admin to set default tool should be straightforward (assign to 2H2024 project)