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Downloading IDR dataset #122

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hamshkhawar opened this issue Sep 16, 2022 · 3 comments
Open

Downloading IDR dataset #122

hamshkhawar opened this issue Sep 16, 2022 · 3 comments

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@hamshkhawar
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@jburel Could you please guide me how can I download images of all the plates IDR screen 102?
you help is appreciated

@jburel
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jburel commented Sep 16, 2022

@hamshkhawar you can find download options at https://idr.openmicroscopy.org/about/download.html
Depending on what you want to achieve other strategies are possible. For example the following notebook analyses a plate using CellProfiler https://github.com/ome/omero-guide-cellprofiler/blob/master/notebooks/idr0002.ipynb without downloading the data on disk.

@hamshkhawar
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hamshkhawar commented Sep 16, 2022

@jburel Thanks for your prompt response. Actually I want to download human High content screening dataset on my local disk and want to process those images on my local disk. I tried docker image to download the example dataset but it throw error
Screen Shot 2022-09-16 at 1 03 17 PM

Aspera Cli is not working for me. Is there an alternative to this?

@jburel
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jburel commented Sep 17, 2022

We have contacted our colleagues at EBI regarding the aspera issue.
we will investigate what's going on with the docker image and get back to you. Thanks for pointing that out

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