Submitting data to the BioImage Archive

Submission to the BioImage Archive currently uses the BioStudies submission system. To submit, you’ll need to register, organise and upload your data and then complete your submission. These steps are explained in more detail below. Before submission you can check whether your data are in scope here.

1. Register an account

You will need to register for a BioStudies account. You can sign up here.

2. Prepare your data

Next, organise your data for submission. Your data files should be in a single directory tree with a logical hierarchical file structure.

3. Upload your data

The easiest way to upload your image files is through the BioStudies submission tool. You can access this through your BioStudies account. For small data volumes, you can use the web upload system - click on “Upload Files”. For larger volumes of data, we would recommend transfer via Aspera or FTP, which you can access via the “FTP/Aspera” button.

4. Add file metadata

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 under what conditions they have been acquired. It can be a tab delimited file (in which case file extension should be “.tsv”), or an Excel file (“.xls” or “.xlsx”).

The first line is a header line, and the first cell has to contain word “Files”. Headers for the other columns are not predefined; we recommend using descriptive, self-explanatory names. Some examples of column headers: Compound, Concentration, Time (for compound treatment experiments), Gene (for genetic variation studies), Plate, Well, Field (for high content screening studies), Channel, Description, QC info. It is useful to include only attributes that have at least two distinct values for the set of image files you are describing in a particular file list; include constant values (e.g., “Organism”) in the annotation of the study entered via the web form.

Use as many lines as there are files in your dataset, and enter the exact filenames in the first column. Note that filenames are case-sensitive. If you have organized files in your BioStudies home directory in a hierarchy, do not forget to reflect that in the file list. E.g., if you have in your home directory folders “ExperimentA” and “ExperimentB”, refer to files inside those folders as “ExperimentA/imageFile1.tif” etc. Fill in attribute values for each of the image files. Do not leave blank lines.

5. Finish submission

When all image files and one or more file lists have been uploaded, go to the “Submissions” section in the submission tool and click “Add new”; select “BioImages” from the list to create an image dataset. Fill in all the necessary fields in the web forms that will be offered, and make sure that the validation panel on the left indicates “all ok”. When that is the case, click on “Submit”. Your submission will be loaded into the BioStudies database and 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, as well as in an e-mail.