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ZauggGroup / DeePiCt

Pipeline for the automatic detection and segmentation of particles and cellular structures in 3D Cryo-ET data, based on deep learning (convolutional neural networks).
Apache License 2.0
29 stars 8 forks source link

test data #20

Closed philsmoot closed 4 months ago

philsmoot commented 4 months ago

Is there test data we can download to use or that matches the 2d_cnn and 3d_cnn sample scripts provided in the README's?

frosinastojanovska commented 4 months ago

Hi @philsmoot, you can use the test data that is provided in the Dropbox folder or the available data from EMPIAR

philsmoot commented 4 months ago

Do you know which EMPIAR image set? i.e. 1, 2, 3…

Thanks, Phil

From: Frosina Stojanovska @.> Date: Thursday, May 2, 2024 at 8:52 AM To: ZauggGroup/DeePiCt @.> Cc: Phil Smoot @.>, Mention @.> Subject: Re: [ZauggGroup/DeePiCt] test data (Issue #20)

Hi @philsmoothttps://github.com/philsmoot, you can use the test data that is provided in the Dropbox folderhttps://www.dropbox.com/sh/oavbtcvusi07xbh/AADmnwIIsLUH1DuJ03IdDO7Ta?dl=0 or the available data from EMPIARhttps://www.dropbox.com/sh/oavbtcvusi07xbh/AABCSionWxE3jHVX7TpwtQqna/Test_data?dl=0&subfolder_nav_tracking=1

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frosinastojanovska commented 4 months ago

I updated the second link, it's EMPIAR-10988

philsmoot commented 4 months ago

Thanks. There are 6 different imaging sets on that page. Is there one in particular I should download?

From: Frosina Stojanovska @.> Date: Thursday, May 2, 2024 at 11:12 AM To: ZauggGroup/DeePiCt @.> Cc: Phil Smoot @.>, Mention @.> Subject: Re: [ZauggGroup/DeePiCt] test data (Issue #20)

I updated the second link, it's EMPIAR-10988

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frosinastojanovska commented 4 months ago

I guess you want the reconstructed VPP or defocus tomograms, since the other files are the files from the tomogram reconstruction steps