Data of submission in the BioImage Archive can be downloaded via web browser, ftp or Aspera. All three methods are explained below. We recommend ftp or Aspera for large download sizes.

Downloading via web browser

Data of a submission can be downloaded via a web browser. First, go to the web page of the specific submission you want to download. Select individual files you like and download by clicking the download button. Otherwise, use the “Download all files” button without selecting any files.

You can also download files that belong to a particular study component of a submission.

Downloading via ftp

The BioImage Archive FTP path is ftp://ftp.ebi.ac.uk/biostudies. Anonymous downloads are enabled. For each study, you can click on the FTP button to access it.

You can also use your favourite FTP client such as FileZilla to download a study from ftp://ftp.ebi.ac.uk/biostudies/<mode>/<path>, where:

<mode> is the storage mode, for some submissions it is nfs and for others it is fire.

<path> is the path of the accession as described above.

You can get the FTP link (including the mode and the path) for a study from the /info REST API endpoint, e.g.,

$ curl https://www.ebi.ac.uk/biostudies/api/v1/studies/S-BIAD570/info -s | jq -r .ftpLink

All data files for a study are in the ftp://ftp.ebi.ac.uk/biostudies/mode/path/Files directory, e.g., to download the file STAN0B0F6_2022-02-25.tiff from S-BIAD570, you can use the command line

$ wget ftp://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/570/S-BIAD570/Files/STAN0B0F6_2022-02-25.tiff

or, for interactive access:

$ ftp ftp.ebi.ac.uk Name: anonymous ftp> cd biostudies/fire/S-BIAD/570/S-BIAD570/Files/ ftp> get STAN0B0F6_2022-02-25.tiff 

Downloading data via Aspera

When downloading large volumes of data, the Aspera protocol can be useful. The information in the section is based on how to transfer files to and from EMBL.

The steps required to use the ascp tool are:

1. Get the ascp command line binary.
   • Download the appropriate aspera transfer sdk for your operating system from: Aspera Transfer SDK - IBM API Hub - IBM Developer
   • Unzip/untar into a suitable directory, for example, C:\aspera on Windows or /opt/aspera on Linux
   • Navigate to the aspera/bin directory. This is the location where you will find the ascp binary.
     
     
2. Get the Public SSH key for use with EMBL-EBI Aspera public account IBM Aspera transfers.

   To use IBM Aspera for downloading public data from EMBL-EBI, you will need the correct private SSH key for authentication. This key has to be saved in a file on your computer and the path to this file will be needed when running the ascp command. The file must have restrictive permissions that allow only the current user to access it. On *nix platforms this is equivalent to mode 0600.
   The key is available for download here and also below:

   
   -----BEGIN OPENSSH PRIVATE KEY-----
   b3BlbnNzaC1rZXktdjEAAAAABG5vbmUAAAAEbm9uZQAAAAAAAAABAAAAMwAAAAtzc2gtZW
   QyNTUxOQAAACAn56FmhbC61KwdCOgiHbyDhYo1JV5LIxaN8XksrUB4UAAAAKg7YRgnO2EY
   JwAAAAtzc2gtZWQyNTUxOQAAACAn56FmhbC61KwdCOgiHbyDhYo1JV5LIxaN8XksrUB4UA
   AAAEAgc79aAbfysxJRwJHSlyNOpNhRgKQApCAc1uYoxTtBuyfnoWaFsLrUrB0I6CIdvIOF
   ijUlXksjFo3xeSytQHhQAAAAIXJvb3RAdHJhbnNmZXJzZXJ2ZXIubXloaXNwZWVkLmNvbQ
   ECAwQ=
   -----END OPENSSH PRIVATE KEY-----
               

   You must save this key to a file on your own machine, e.g. /home/user/.ssh/aspera-public-private-key.key with permissions 0600 (on *nix - chmod 600 <path to key>). You will need the path to this key when executing the ascp command.

3. Get the path to the file(s) you want to download.
   • Get the common root for all files in the study:

     
     curl https://www.ebi.ac.uk/biostudies/api/v1/studies/<accession id>/info -s | jq -r .ftpLink | sed 's#ftp://ftp.ebi.ac.uk##g'
                     

     e.g. for S-BIAD2119:

     
     curl https://www.ebi.ac.uk/biostudies/api/v1/studies/S-BIAD2119/info -s | jq -r .ftpLink | sed 's#ftp://ftp.ebi.ac.uk##g'
                     

   • Get the relative path to individual files from the file list of the relevant study component of the study.
   • Form the path for a file by

     
     <common root>/Files/<relative path to individual file>
                     

     e.g.

     
     /pub/databases/biostudies/S-BIAD/119/S-BIAD2119/Files/microscopy_image/microscopy_image/TH_sympathetic_nerve/sample1/slice_0000.tif
                     

     The example above comes from a study on 'nfs' at the time of writing. If the study is on 'fire' (our FIle REplication service), the path will be of the form

     
     /biostudies/fire/S-BIAD/570/S-BIAD570/Files/STAN0B0F6_2022-02-25.tiff
                     

     Following the steps above should give the correct path regardless of whether the study is on nfs or fire.
     
     
4. Download the file(s).

   Assuming you are in the aspera/bin directory, your command for download should be like this:

   
   ./ascp -P33001 -Q -l 300M -i <key> fasp-public@fasp.ebi.ac.uk:<file to download> <download location on your machine>
           

   Where
   • -P33001 and fasp-public@fasp-beta.ebi.ac.uk define the port, user and server for the Aspera connection.
   • <key> is the path to the public key for use with the EMBL-EBI Aspera connection (see subsection above).
   • <file to download> is the remote download path (see subsection above).
   • -Q enables quiet mode suppressing progress output and logs, so the command runs more silently.
   • -l 300M sets the target transfer rate limit to 300 megabits per second.
   For instance, here’s the command line to download the file microscopy_image/microscopy_image/TH_sympathetic_nerve/sample1/slice_0000.tif from submission S-BIAD2119 to the directory ~/temp on linux:

   
   ./ascp -P33001 -Q -l 300M -i ~/.ssh/aspera-public-private-key.key fasp-public@fasp.ebi.ac.uk:/pub/databases/biostudies/S-BIAD/119/S-BIAD2119/Files/microscopy_image/microscopy_image/TH_sympathetic_nerve/sample1/slice_0000.tif  ~/temp/
           

Downloading data using Globus

The BioImage Archive supports file downloads through Globus as well. You can click on the Globus icon to open up the EMBL-EBI Public Data collection in the Globus File Manager app. You may want to install Globus Connect Personal which creates a personal collection on your machine for transferring multiple files.