From 53ee3f4f8f771786fd5907f0319e058c7c7aa376 Mon Sep 17 00:00:00 2001 From: d33bs Date: Wed, 21 Jan 2026 14:57:48 -0700 Subject: [PATCH 1/4] add bioimage archive upload process --- README.md | 21 +++++++------- internal/bioimage_archive_upload.md | 45 +++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+), 10 deletions(-) create mode 100644 internal/bioimage_archive_upload.md diff --git a/README.md b/README.md index 779e4a3..e0bf32a 100644 --- a/README.md +++ b/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. | diff --git a/internal/bioimage_archive_upload.md b/internal/bioimage_archive_upload.md new file mode 100644 index 0000000..8fda5ed --- /dev/null +++ b/internal/bioimage_archive_upload.md @@ -0,0 +1,45 @@ +# 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. + +## 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. + +2. Login or create account on the [BioImage Archive login page](https://www.ebi.ac.uk/biostudies/submissions/signin) (accounts are free to create). + +3. 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. + +4. 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. + +5. 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. + +7. 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). + +7. If you run into trouble or questions, reach out to bioimage-archive@ebi.ac.uk to help address issues. + +9. 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. From 6ce7816a9052912aa61ba3d063e50326bea5c459 Mon Sep 17 00:00:00 2001 From: d33bs Date: Wed, 21 Jan 2026 16:53:45 -0700 Subject: [PATCH 2/4] linting --- internal/bioimage_archive_upload.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/internal/bioimage_archive_upload.md b/internal/bioimage_archive_upload.md index 8fda5ed..246c9a1 100644 --- a/internal/bioimage_archive_upload.md +++ b/internal/bioimage_archive_upload.md @@ -20,13 +20,13 @@ Use this guide when a project is ready to publish raw image data and the authori 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. -2. Login or create account on the [BioImage Archive login page](https://www.ebi.ac.uk/biostudies/submissions/signin) (accounts are free to create). +1. Login or create account on the [BioImage Archive login page](https://www.ebi.ac.uk/biostudies/submissions/signin) (accounts are free to create). -3. 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. 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. -4. 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. 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. -5. Generate "study component" for uploaded files with (one for each type of file). +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: @@ -38,8 +38,8 @@ filename.tif image/tiff 7225258 6. Submit for review and record the accession ID. -7. 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. 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). -7. If you run into trouble or questions, reach out to bioimage-archive@ebi.ac.uk to help address issues. +1. If you run into trouble or questions, reach out to bioimage-archive@ebi.ac.uk to help address issues. -9. 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. +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. From 5c72545a292e5dfd7e8179acb07693bd9a52b036 Mon Sep 17 00:00:00 2001 From: Dave Bunten Date: Thu, 22 Jan 2026 16:01:51 -0700 Subject: [PATCH 3/4] Update internal/bioimage_archive_upload.md Co-authored-by: Gregory Way --- internal/bioimage_archive_upload.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/internal/bioimage_archive_upload.md b/internal/bioimage_archive_upload.md index 246c9a1..e9d216c 100644 --- a/internal/bioimage_archive_upload.md +++ b/internal/bioimage_archive_upload.md @@ -38,6 +38,8 @@ 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. If you run into trouble or questions, reach out to bioimage-archive@ebi.ac.uk to help address issues. From 570b1237252939950e1d40754a6f7c2877d5d5e2 Mon Sep 17 00:00:00 2001 From: d33bs Date: Thu, 22 Jan 2026 16:05:59 -0700 Subject: [PATCH 4/4] add callout for email support Co-Authored-By: Gregory Way --- internal/bioimage_archive_upload.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/internal/bioimage_archive_upload.md b/internal/bioimage_archive_upload.md index e9d216c..2766c53 100644 --- a/internal/bioimage_archive_upload.md +++ b/internal/bioimage_archive_upload.md @@ -11,6 +11,10 @@ It hosts raw image datasets with stable accession IDs so others can find, access 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). @@ -42,6 +46,4 @@ filename.tif image/tiff 7225258 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. If you run into trouble or questions, reach out to bioimage-archive@ebi.ac.uk to help address issues. - 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.