Submitting data to the BioImage Archive

IMPORTANT NEWS: The submission tool has been updated. The metadata fields have not changed but the appearance and functionality of the submission tool has changed. Please read this page first and check the online tutorial to learn about how to submit using the new submission tool. There is also a short demo video on this page and how-to documentation under the Help tab in the new Submission Tool. If you have any problems please contact us.

Submission to the BioImage Archive currently uses the BioStudies submission system, when you start a BIA submission you will be redirected to their service. Before submission you can check whether your data are in scope here.

To submit, you’ll need to register an account, organise and upload your data, prepare a file list, and then submit using our web submission form. These steps are explained in more detail below.

You can also submit annotations, i.e. segmentation masks, meshes etc., with or without including the source images. If your submission contains only images, or images and their corresponding annotations please follow the steps below. If you are submitting only annotations for an existing image dataset follow the instructions here.

If you are submitting spatial transcriptomics data, please check this page with detailed guidelines.

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 like composite images or segmentation masks etc. Your data files should be in a single directory tree with a logical hierarchical file structure. Please note that the file paths are not visible on the submission web page, therefore if there is embedded information in the directory structure please put that information as metadata in the file list (see step 4).

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. We also cannot have single files larger than 2TB, and would recommend keeping individual files under 100GB as that will make the upload process faster and less brittle to errors. Please also check this page if you’re submitting zarr or ome-zarr files.

Uploading large datasets takes time so please make sure you plan your submission with sufficient time. For data sets > 10 Tb, please contact us first, as arrangements might be needed in order to accommodate very large datasets. As we have a hard limit of 2 Tb file size per file, submitting your data in multiple chunks and/or zipping it might be a more feasible option. You can upload part of your data, create a new submission, and set up a release date into the future, and click on Submit. Once it is processed, and you are happy with it, you can add the rest of your data. You will need to amend your file list(s) to reflect the new data additions and re-submit.

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. Upload your data

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

Please note that we cannot accept single files larger than 2TB.

The FTP/Aspera tab in the submission tool upload section will include your credentials and upload guidance for these two upload methods.

4. Prepare your file list

Each study component and annotation section must have a file list. These are used to describe the files you wish to include in your submission associated with the relevant component, including image files, annotations, and other supporting files e.g., analysis results such as a spreadsheet containing cell areas. If you have annotations, e.g. segmentations masks, point annotations etc., the file list for that annotation component should also include a “source_image” column to reference the original image that has been annotated. The purpose of file lists is to provide information that will help the users of your dataset understand what different files mean and specify file level metadata. A file list can be a tab delimited file (in which case file extension should be “.tsv”), or an Excel file (“.xls” or “.xlsx”).

Please read the File List help page for details of what should be included in the file list before continuing with this guide.

5. Submission

When all images and related files and file lists have been uploaded, you can create your submission here. Make sure you select the BioImage Archive Submission template when creating a new submission. This is to submit images and image related data, or images and annotations. For annotations-only submissions without corresponding images, please follow the submission instructions here.

Fill in all the necessary fields in the web forms that will be offered. You can also add sections to your submission if necessary. Make sure that the validation panel on the left indicates “all ok”. When that is the case, click on “Submit”.

If you are submitting spatial-omics or correlative imaging datasets where the omics data or volume EM data are in other archives, please link to those using the link field. For more guidance check here.

If you have any problems please contact us.

Here is a 2 minute submission demo video:

After your submission is loaded into the BioImage Archive database, it will be assigned a unique BioImage Archive accession number (i.e., dataset identifier). The accession number will be the same before and after making the dataset public and will not change even if revisions are necessary. 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’.