benchos-gel-annotator

name	benchos-gel-annotator
description	Review gel or blot images in the BenchOS Gel Annotator, add ladder or lane annotations, quantify bands with ROI boxes or line profiles, and persist exports back into notebook entries.
license	Proprietary
compatibility	Requires BenchOS with the website Tools page enabled plus standard BenchOS entry or registry attachment APIs for persistence.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS Gel Annotator

Use this skill when the user wants to:

• annotate a gel or blot image with notes, lane labels, or ladder labels
• quantify one or more bands from a selected ROI
• inspect a line-profile intensity trace across a lane
• save a raw, adjusted, or annotated export back into BenchOS

Browser Tool First

BenchOS exposes this workflow in the website Tools page as Gel Annotator. Prefer the browser tool whenever the user needs interactive ROI placement, draggable notes, or visual export review.

Use this skill when the user needs agent help to:

• decide which ROIs or lanes to quantify
• summarize what should be annotated before upload
• attach the resulting export to a BenchOS notebook entry or registry item

Expected Workflow

1. Ask for the gel image file and whether the user wants annotation, quantification, or both.
2. Direct the user to the Gel Annotator browser tool for the actual interactive selection work.
3. Ask which export variant they want persisted:
   • raw
   • color adjusted
   • annotated
4. If the user wants BenchOS persistence, upload the exported file through the normal attachment APIs.
5. If the user wants the image placed into a notebook entry, append a short HTML block after uploading the attachment.

Measurement Guidance

• Treat display brightness and contrast as presentation-only adjustments unless the user explicitly asks to apply transformed pixels for downstream analysis.
• For dark bands on a light background, prefer signal interpretation as 255 - intensity.
• For light bands on a dark background, use the direct intensity profile.
• ROI boxes are appropriate for mean and integrated signal over a band.
• Line selections are appropriate for full lane or band profile inspection.

BenchOS Persistence Options

• Entry attachments: POST /api/entries/:id/attachments
• Registry attachments: POST /api/registry/:id/attachments
• Entry note append: POST /api/entries/:id/append

Notes

• The current BenchOS implementation is intentionally browser-native and modeled on Fiji/ImageJ gel-analysis interaction patterns rather than shipping the desktop Fiji stack inside the runtime.
• Use SVG or PDF exports when the user wants downstream editing in Illustrator or presentation software.