Pro Tools and Advanced Science

Pro Tools and advanced science

Pro Tools keeps specialist workspaces in one place so the normal editor stays usable.

The exact list can grow as FigureLoom develops, but the main workspaces are described below.

Arrange and group

Use Arrange and group for multi-object layout.

Tools include:

• Shift-click and marquee selection
• Multi-object movement
• Multi-object corner resizing
• Group and ungroup
• Align
• Distribute
• Smart guides
• Edge snapping
• Anchored connectors

Grouped objects remain separate editable layers.

Data and charts

Create or edit tables and plots from pasted or imported data.

Typical actions include:

• Paste CSV or tab-separated cells
• Choose chart type
• Insert editable table
• Reopen source data
• Change chart title
• Replace data without rebuilding the entire page

See Data, tables, and charts.

Scientific annotation

Annotation tools include:

• Panel labels
• Callouts
• Scale bars
• Measurement lines
• Significance brackets
• Grouping brackets
• Numbered markers
• Legends
• Greek symbols
• Superscript and subscript
• Chemical-number formatting

For complete TeX rendering, use the TeX workspace.

Components and objects

A component is a reusable selection stored inside the project.

Use components for repeated elements such as:

• Sample icons
• Panel headers
• Treatment boxes
• Legend keys
• Repeated pathway nodes
• Lab-specific symbols

Actions include:

• Save selection as component
• Insert another instance
• Update project instances from a revised selection
• Crop, flip, and mask images
• Apply simple Boolean operations to native shapes

Review and references

Review tools support:

• Comments on objects or pages
• Resolve and reopen states
• Navigation to comments
• DOI, creator, source, URL, license, attribution, and notes
• Automatic reference collection from used artwork
• Downloadable reference list
• Named checkpoints
• Change highlighting
• Alt-text drafting
• Contrast and text-size checks
• Grayscale and color-vision previews

See Review, references, and accessibility.

Publish and present

Publishing tools include:

• Generic journal-size presets
• Readiness checks
• Downloadable readiness report
• Fullscreen multi-page presentation
• Export diagnostics
• Compatibility warnings

The current visual export path uses editable SVG for the active page or every project page. Convert a checked SVG elsewhere when another file format is required.

FigureLoom does not guarantee compliance with a journal, printer, or conference. Check current requirements yourself.

Office bridge

The office workspace imports supported PowerPoint and spreadsheet files.

PowerPoint import can recover many common elements such as:

• Text
• Shapes
• Images
• Tables
• Groups
• Basic charts

Spreadsheet import supports common workbook and delimited formats.

The current export panel does not create a PowerPoint file. Use SVG and convert it in another application when a presentation file is required.

See Importing PowerPoint and spreadsheets.

Workspace and recovery

Workspace tools include:

• Move or copy objects between pages
• Project asset management
• Broken-asset checks
• Recovery snapshots
• Pre-export diagnostics
• Workspace reset
• Shortcut reference

Use a project backup before deleting assets or resetting a workspace.

Advanced Science

Advanced Science provides starters and specialist layouts for work that would be tedious to assemble from scratch.

Available areas can include:

• Publication plot starters
• Sequence tracks
• Protein-domain tracks
• Phylogenetic trees
• Gel and blot lanes
• Microscopy channel layouts
• Specialist biological and environmental diagrams

These are layout tools. Validate scientific analysis in the appropriate specialist software.

Accounts and gallery

Account tools include:

• Local gallery without an account
• Email and password account creation
• Confirmation and password recovery
• Encrypted owned and shared cloud gallery
• Profile picture or initials
• Explicit cloud save actions

See Accounts, cloud projects, and collaboration.

Live collaboration

Collaboration tools include:

• Owner, editor, reviewer, and viewer roles
• Named presence and remote cursors
• Encrypted project broadcasts
• Persistent review comments
• Email-account invitations
• Expiring guest links
• Guest joining with a display name and no email account
• Optional 4 to 12 digit guest-link PIN
• Remote-update conflict controls

Incoming edits pause while the local user is typing or dragging.

MCP and AI access

MCP is configured from Settings rather than the Pro Tools hub, but it can use the normal editor and specialist commands that are registered in the open project.

The hosted connection supports:

• A private project-specific connection link
• Read-only or full editor access
• A separate destructive-action permission
• Current command discovery
• Normal Undo history and saving for successful writes
• Disconnect, reconnect, and revocation

MCP is optional and separate from Loomy. See MCP and AI access.

SVG path editor

The path editor can inspect and change SVG path command data.

It supports:

• Viewing commands and coordinates
• Selecting anchors
• Editing values
• Breaking compound SVG artwork into independent SVG objects

It is not a full desktop Bezier editor.

TeX typesetting

The TeX workspace uses MathJax on demand.

It supports:

• TeX source
• Inline or display mode
• Color control
• SVG rendering
• Retained source for later editing

See Equations, code, and scientific notation.

Pathway exchange

The active page can be exported as starter machine-readable pathway structures:

• SBGN-ML
• BioPAX RDF/XML
• SBML Level 3 XML

FigureLoom maps objects and connectors into these structures. The output should be opened and validated in a specialist pathway tool before scientific use.

Optional prompt interpretation

Loomy can use a deterministic layout system and, in supported deployments, optional prompt interpretation.

The ordinary editor does not depend on Loomy or a language model.

See Loomy.

When to use Pro Tools

Use Pro Tools when:

• Several objects need exact arrangement.
• Data should remain editable.
• A figure needs formal review or references.
• You need recovery or asset diagnostics.
• A specialist starter can save setup time.
• You are preparing publication output.

Stay in the normal editor when the task only needs text, shapes, images, arrows, and basic formatting.