Gel Annotator - Operator Manual

Author: Felix Gerlach
Bug reports: felixgerlach@yahoo.de

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1. Purpose

This application is for:

• loading one or multiple gel/blot images,
• optionally extracting multiple panels,
• composing panels into one figure,
• annotating lanes, headers, brackets, highlights, and marker ticks,
• running optional lane intensity / band-size analysis,
• exporting publication-ready output.

The workflow is step-based and stateful.

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2. Quick Start

1. Open the app.
2. In Step 1, choose mode and image(s).
3. If you use multi-panel or multi-image workflows, complete Step 2a/2b.
4. Edit image in Step 3.
5. Set lanes and gel region in Step 4.
6. Optionally add highlights in Step 4b.
7. Add headers/brackets in Step 5.
8. Assign marker ticks in Step 6.
9. Optionally run analysis in Step 6b.
10. Finalize/export in Step 7.

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3. Workflow Reference

Step 1 - Session Settings

Main controls:

• Experiment type
• Panel mode (single or multi_panel)
• Source mode (single_image or multi_image)
• Default marker unit (bp / kDa)
• Invert preference
• Keep settings for next image
• UI theme color
• Image selector buttons
• Readme / Help button

Step 2a - Panel Selection from Source Images (mode-dependent)

Used when selecting multiple panels before composition.

Functions:

• select source image,
• rotate source (Apply, +/-90, +/-1),
• draw panel rectangles,
• assign panel metadata:
  • marker panel flag,
  • scaling group ID.

Result:

• selected crops + metadata are passed to compose step.

Step 2b - Compose Multiple Panels/Images (mode-dependent)

Functions:

• drag panels,
• rotate (+/-90, +/-1),
• scale X/Y,
• color preprocessing per panel (B/C/G, WB, invert, B/W),
• align/scaling using marker-based workflow,
• optional final crop with undo.

Step 3 - Edit

Functions:

• brightness / contrast / gamma,
• WB / invert / B/W,
• rotation (Apply, +/-90, +/-1),
• crop and reset edits.

Step 3b - Panel Selection from Single Edited Image (mode-dependent)

Functions:

• draw one or more crop rectangles from the edited image.

Step 4 - Panel Layout

Functions:

• set lane count,
• marker lane index,
• define gel region(s) and lane counts per region,
• choose whether optional highlight step is enabled.

Display:

• lane boundaries + lane numbers in circles are shown over preview.

Step 4b - Band Highlights (optional)

Enabled only when Step 4 checkbox is active.

Highlight shapes:

• box
• arrow (filled arrow head)
• asterisk

Controls:

• color,
• line width,
• apply style to existing highlights,
• remove last / clear all.

Step 5 - Header / Column Annotation

Functions:

• add/remove header rows,
• per-row:
  • row name,
  • top/bottom position,
  • angle,
  • heading font size,
  • value font size,
• bracket groups (lane ranges + labels),
• bracket text distance,
• per-element offsets,
• top-annotation order editing.

Step 6 - Marker / Ladder

Functions:

• choose marker definition (library/new/edit),
• assign tick positions by selecting a tick then clicking panel,
• override / clear / hide / show marker ticks,
• marker style controls:
  • X/Y offsets,
  • tick length,
  • label gap,
  • marker font size.

Option:

• Run lane intensity/band analysis before review.

Step 6b - Lane Intensity and Band Analysis (optional)

Functions:

• lane profile/histogram view,
• lane overlay + marker fit view,
• peak detection controls:
  • threshold,
  • prominence,
  • min distance,
  • smoothing window,
  • polarity,
• optional background correction using selected empty lane,
• fit model select:
  • monotone interpolation,
  • log-linear regression,
  • log-quadratic regression,
• save analysis report.

Step 7 - Review and Export

Functions:

• inspect final rendered image,
• interactive element editing on selected items:
  • position,
  • color,
  • font,
  • size,
  • angle/orientation,
  • line/tick/bracket styling,
• save final output

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4. Important Defaults (current)

Selected core defaults in current version:

• panel lanes default: 10
• marker label font size default: 15
• bracket text distance default: 10
• highlights default: disabled
• highlight style default: box
• analysis defaults:
  • threshold 20
  • prominence 7
  • min distance 10
  • smoothing 10
  • fit mode Monotone interpolation

When background correction is enabled in analysis, workflow-specific reduced defaults are applied (threshold=3, smoothing=5).

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