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Upload a dataset

This section will guide you how to upload data to CryoCloud - either via our web application, sftp or using CC'Up.

We recommend using [CC'Up](/docs/Upload a dataset#dataset-upload-via-ccup) for the fastest and most convenient upload experience (under development).

Dataset Upload via CC'Up​

The CryoCloud Uploader (CC Up) is a standalon application that allows for the fastest and most stable upload from any system. You can Download CC'Up here:

Download CC Up for Windows here

Download CC Up for Mac OS here

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Please note that these are beta versions that are not signed yet with the Windows & Mac stores. After downloading the software, please click "Run anyway" for windows during the installation process to complete the installation. For Mac OS run the following command after moving the app to Applications: xattr -d com.apple.quarantine /Applications/CryoCloud\ Uploader.app

After completing installation, you can login with your credentials. You will then see an overview of all your existing datasets similar to the web-application. To create a new dataset, Click the "+" on the top left and specify a dataset name, type & file format (e.g. movies & .tiff). To upload new files,simply follow the steps below:

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  1. Open the new dataset by clicking "Manage". In the second tab, (1) Create release, specify the image parameters and confirm with "Create Release" on the bottom right.

  2. In the tab (2) Upload Asssets, specify whether you only want to upload files of the file type specified for the dataset (e.g. .tiff), and whether you want a live upload (i.e. monitor a folder and conitnously upload new files) or upload individual files. Please note: for a static you have to select one or multiple files, for live upload you have to select a folder.

  3. If a live upload is finished and you don't expect more files, you can terminate the live upload by clicking "Mark as completed".

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  1. You can add more files or folders by adjusting the toggle and selecting more files for upload. (e.g. if you have a .mrc gain reference, but a .tiff dataset format, untoggle "Check file type" and select the .mrc gain file.
  2. You can inspect the uploaded files in tab 4.
  3. If all your files have been uploaded, finalize the dataset by clicking "Finalize Release" in the last tab. This step is similar to the Import step in Relion, and will create a star file that you can use for analysis in a new project.

Dataset Upload via web application​

We recommend files uploads via the web application for individual files and small datasets up to 100GB. Click on the **Dataset** tab on the left, and then +New dataset on the top right. Specify dataset name, dataset type (e.g. movies or aligned frames) and file format (.tif(f), .mrc)

Once the dataset is created, create your first release by following these steps:

  1. Fill out the optics parameters and add a note (optional).
  2. Starfile creation: If you upload movies and want to start analysis with motioncorrection click yes. Select “No” if you want to upload your own starfile for aligned micrographs, movies or particles.
  3. Click “Create draft release”.
  4. Upload files in the next tab, inspect the files in the file browser and click finalize release. If you want to update your release, simply adjust the parameters, click draft release and upload more files if you like. Once you are done, click ‘Finalize release’
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Releases keep track of your dataset versions, in particular the associated movies or particles.star files. This is handy if you want to add more files or change some of the parameters later on, e.g. if you made a mistake.

Dataset upload via sftp​

If you prefer uploading large amounts of data via the commandline using sftp, please contact us. We can set up a sftp server for you and provide you with the credentials for data upload.