Add BioImage Archive upload process

README.md

@@ -7,13 +7,14 @@ See the GitHub Pages version of this content here: [https://wayscience.github.io
 Top-level playbooks have information which may be relevant to other computational labs.
 Playbooks in the `/internal` folder have information specific to the Way Lab.
 
-| Playbook                                           | Type     | Description                                                                 |
-| -------------------------------------------------- | -------- | --------------------------------------------------------------------------- |
-| [Code Strategy](code_strategy.md)                  | General  | Strategy for using and writing code in a scientific setting.                |
-| [Conference Playbook](conference_playbook.md)      | General  | Playbook for selecting and participating in conferences.                    |
-| [Data Strategy](data_strategy.md)                  | General  | Strategy for using and storing data; includes our 3 data perspectives.      |
-| [GitHub Strategy](github_strategy.md)              | General  | Strategy for using GitHub efficiently; details our 3 types of repositories. |
-| [Calendar Playbook](internal/calendar_playbook.md) | Internal | Playbook for joining and using Way Lab calendar.                            |
-| [Computer Setup](internal/computer_setup.md)       | Internal | Instructions for lab computer setup.                                        |
-| [Onboarding](internal/onboarding.md)               | Internal | Onboarding materials for the Way Lab.                                       |
-| [Remote Access](internal/remote_access.md)         | Internal | Instructions for remotely connecting to and using Way Lab computers.        |
+| Playbook                                                       | Type     | Description                                                                 |
+| -------------------------------------------------------------- | -------- | --------------------------------------------------------------------------- |
+| [Code Strategy](code_strategy.md)                              | General  | Strategy for using and writing code in a scientific setting.                |
+| [Conference Playbook](conference_playbook.md)                  | General  | Playbook for selecting and participating in conferences.                    |
+| [Data Strategy](data_strategy.md)                              | General  | Strategy for using and storing data; includes our 3 data perspectives.      |
+| [GitHub Strategy](github_strategy.md)                          | General  | Strategy for using GitHub efficiently; details our 3 types of repositories. |
+| [Calendar Playbook](internal/calendar_playbook.md)             | Internal | Playbook for joining and using Way Lab calendar.                            |
+| [Computer Setup](internal/computer_setup.md)                   | Internal | Instructions for lab computer setup.                                        |
+| [BioImage Archive Upload](internal/bioimage_archive_upload.md) | Internal | Minimal guide to uploading datasets to the BioImage Archive.                |
+| [Onboarding](internal/onboarding.md)                           | Internal | Onboarding materials for the Way Lab.                                       |
+| [Remote Access](internal/remote_access.md)                     | Internal | Instructions for remotely connecting to and using Way Lab computers.        |

internal/bioimage_archive_upload.md

@@ -0,0 +1,49 @@
+# BioImage Archive Upload
+
+This is a short, practical guide to uploading datasets to the BioImage Archive.
+
+## What is BioImage Archive?
+
+BioImage Archive is a public repository for biological imaging data.
+It hosts raw image datasets with stable accession IDs so others can find, access, and reuse the data tied to a publication or project.
+
+## When to use this
+
+Use this guide when a project is ready to publish raw image data and the authoring team has decided to deposit in the BioImage Archive.
+
+## If you run into questions or issues
+
+> ⚠️ If you run into trouble or questions, reach out to [bioimage-archive@ebi.ac.uk](bioimage-archive@ebi.ac.uk) to help address issues.
+
+## Prerequisites
+
+- A finalized dataset folder (no in-progress changes).
+- A metadata sheet with sample, imaging, and experimental details (or manuscript with these details)
+
+## Quick steps
+
+1. Organize files into a single local submission folder. If the files are stored on a network share, consider copying them locally to ensure the transfer to BioImage Archive is seamless.
+
+1. Login or create account on the [BioImage Archive login page](https://www.ebi.ac.uk/biostudies/submissions/signin) (accounts are free to create).
+
+1. Upload files using ["files" tab](https://www.ebi.ac.uk/biostudies/submissions/files) (bulk uploads require Aspera or FTP). The bulk connection information unique to your account is available under the "FTP/Aspera" button. Note: you can use [`rclone`](https://rclone.org/ftp/) here to help manage the FTP connection transfers from the command line.
+
+1. Fill out a new submission from the ["submissions" tab](https://www.ebi.ac.uk/biostudies/submissions/). Note: you can copy and paste fields into a Google Doc (or another service) for verification with your authoring team.
+
+1. Generate "study component" for uploaded files with (one for each type of file).
+
+You'll need to generate a `.tsv` file like this for the field:
+
+```tsv
+Files   File Type   File Size
+filename.tif    image/tiff  7225258
+...
+```
+
+6. Submit for review and record the accession ID.
+
+## After submission
+
+1. Watch the ["submissions" tab](https://www.ebi.ac.uk/biostudies/submissions/) for challenges with your upload (it will show an icon indicating there's an issue which needs to be resolved if something comes up).
+
+1. Once the submission is successful you'll have access to a link which [looks like this](https://www.ebi.ac.uk/biostudies/studies/S-BIAD2515) from the "submissions" tab.