Submitting data to the BioImage Archive

Submission to the BioImage Archive currently uses the BioStudies submission system. Before submission you can check whether your data are in scope here .

To submit, you’ll need to register, organise your data and prepare a file list, upload your data and then complete your submission. These steps are explained in more detail below:

1. Register an account

You will need to register for a BioStudies account. You can sign up here and then return to this guide.

2. Prepare your data

Now, organise your data for submission. Please include everything needed to reproduce your results. This might be raw data, intermediate results or processed data. Your data files should be in a single directory tree with a logical hierarchical file structure (see figure).

Please note that some special characters are not allowed in directory and file names. Stick to the allowed characters listed here to avoid any problems with your submission.

For any program code accompanying your study, it is best to upload that code to a specialised repository (e.g. GitHub or Gitlab), and then add a link to it in your submission, which you will be able to do during the submission process.

The BioImage Archive implemented Recommended Metadata for Biological Images (REMBI) metadata guidelines to further support FAIR sharing. You will need to provide REMBI level metadata of your study at the final step of the submission process, using the BIA web submission tool. REMBI guidelines are also useful to plan on what to include and how to organise your data. Please check the more detailed overview of REMBI metadata here and how to organise your submission into REMBI Study Components .

3. Prepare your file list

You will need a “table of contents” for your image files, called a “File List” in the submission tool. The purpose of this file is to provide information about the individual image files that will help the users of your dataset understand what different files mean and specify file level metadata. It can be a tab delimited file (in which case file extension should be “.tsv”), or an Excel file (“.xls” or “.xlsx”). We recommend editing using a spreadsheet software (Google Sheets, Excel, LibreOffice), and then exporting as tsv and uploading the export.

Please check the File List help page and then return to this guide.

4. Upload your data

We support multiple methods of data upload, each recommended if the submission size falls within one of the following ranges:

For detailed guidance on how to fill the submission form, how to add sections and edit your submission, please check the Submission subsection of BIA online tutorial.

After your submission is loaded into the BioStudies database, it will be assigned a unique BioImage Archive accession number (i.e., dataset identifier); details on how to access and share your study with others will be available in a confirmation window and will also be sent via e-mail. Your submission will however only be visible to you until its ‘Release Date’.