Uploading files

How do I upload files to the platform?

Files on the Blackfynn platform always belong to a dataset and it is not possible to share files between datasets, or to copy files from one dataset to another dataset.

After uploading files, the platform automatically groups files that belong together. This collection of files shows up in the platform as a single file. This happens when a single file format consists of multiple files (e.g. many DICOM files within a single clinical image). Even though the set of files shows up as a single object in the platform, all source files are retained and are available for download.

Once you have created a dataset there are a number of ways to upload files to the dataset.

Using the Web Application

All files are located in the Files tab within a dataset. This is the main location where all files are organized.

Using the Files tab

Within a dataset, you can navigate to the Files tab. This is the main location where all files are organized.

In the Files tab, you can create folders to organize your files on the platform.

To upload files, you can drag files from your local machine directly into the file browser panel. A popup window will show the files that will be uploaded.

If you’ve enabled automatic processing, your data will be processed once it’s uploaded to the platform. Depending on the data modality and size, this process can take a while.

Note that two of the files in the example below are combined as they belong to the same timeseries package.

Click Start Upload to begin uploading the files. During the upload process, you can safely hide the popup window as files will continue to be uploaded in the background.

Once files are uploaded to the platform, they will show up in the file browser. Depending on the file format, the platform will process the data to enable the data to be viewed in the browser based data viewer. Processing of the data can take a while and you will be notified when this has completed.

Linking to External Files

If you have limited uploading capabilities, or you’d just prefer to keep your data on an existing system, you can link to an external file. External files allow you to create a symbolic link to data that exists outside of Blackfynn. You can keep your data on a third-party service like Dropbox or Box.net and still be able to use the modeling and relationship capabilities Blackfynn offers.

Go to your Files tab and click Add File and select Link to External File.

You can represent your files as an external link without having to upload any actual data.

Directly to records

You can also upload files directly to a metadata record. After creating the record, drag one or more files to the drop-box in the record details page. In the example below, the file will be uploaded to the platform and automatically be associated with Experiment 1 .

You can always associate files with metadata records after the files are uploaded to the platform, as well as remove any association between files and specific metadata records.


You can upload files programmatically using one of our client tools (see developer documentation).

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