pepkio-figure-panel-mockup-grid

Programmatic layout grid generator and alignment client for constructing journal-compliant multi-panel scientific figures with automated column width validation.

What It Does

pepkio-figure-panel-mockup-grid provides a Python interface to programmatically design, scaffold, and validate multi-panel figure layouts for scientific publication (Nature, Cell, Science, PNAS, and EMBO Journal). It automates panel grid calculations across 1-column, 1.5-column, and 2-column specifications, enforces aspect ratio limits, aligns heterogeneous experimental panels, validates canvas dimensions against publisher guidelines, and exports structured asset inventory manifests.

Features

• Journal Column Scaffolding: Automatically calculate panel grid geometry matching Nature, Cell, Science, and PNAS column width standards.
• Programmatic Panel Alignment: Align panels along top, left, bottom, or right edges and distribute horizontal/vertical spacing evenly.
• Aspect Ratio Control: Enforce fixed aspect ratios (1:1, 4:3, 3:2, 1:2, or free) to prevent distortion of micrographs and blot crops.
• Experimental Metadata & Scale Bars: Tag panels (blot, graph, micrograph, scatter, blank), attach imaging notes, and manage physical scale bar properties.
• Layout Validation Engine: Check composite layouts against maximum page height, margin limits, and panel overlap constraints.
• Inventory Table Export: Export figure panel asset inventories and coordinate specifications in Tab-Separated Values (TSV) or Markdown format.
• CLI & Python API: Execute layout scaffolding and validation programmatically or via command-line tools.

Installation

pip install pepkio-figure-panel-mockup-grid

Quick Example

from pepkio_figure_panel_mockup_grid import PepkioClient

# Initialize the Pepkio API client
with PepkioClient(api_key="YOUR_API_KEY") as client:
    # 1. Scaffold a 2x3 grid layout for a Nature 2-column figure (170 mm)
    scaffold_input = {
        "action": "scaffold",
        "rows": 2,
        "cols": 3,
        "document": {
            "journal": "nature",
            "columnWidth": "2-col",
            "marginMm": 3.0,
            "gapMm": 2.5,
            "labelStyle": "uppercase",
        },
    }
    scaffold_res = client.run(scaffold_input)
    document = scaffold_res.result["document"]

    # 2. Add panel type tags, imaging notes, and scale bar settings
    document["panels"][0]["typeTag"] = "micrograph"
    document["panels"][0]["facilityNote"] = "Confocal GFP staining (63x Oil)"
    document["panels"][0]["showScaleBar"] = True
    document["panels"][0]["scaleBarLength"] = "10 µm"
    document["panels"][0]["aspectLock"] = "1:1"

    # 3. Validate layout geometry against Nature publisher limits
    val_res = client.run({"action": "validate", "document": document})
    print("Layout Valid:", val_res.result.get("valid", True))

    # 4. Export the figure panel inventory as a Markdown table
    table_res = client.run({"action": "export_table", "format": "markdown", "document": document})
    print("\nFigure Inventory Table:\n")
    print(table_res.result["table_text"])

Typical Use Cases

• Manuscript Composite Figure Assembly: Plan 2-column composite figures combining Western blot crops, qPCR graphs, and confocal microscopy grids for manuscript submission.
• Microscopy & Immunofluorescence Layout Planning: Scaffold multi-channel immunofluorescence grids (Control vs. Treatment) with enforced 1:1 square aspect ratios and $10\ \mu\text{m}$ scale bars.
• Western Blot Gel Crop Alignment: Structure multi-antibody blotting experiments with aligned gel band panels, ladder lane positions (kDa), and corresponding densitometry graphs.
• Flow Cytometry & Gating Panels: Arrange multi-sample gating scatter plots, UMAP dimensionality reduction projections, and population charts into uniform grids.
• Asset Inventory & Lab Notebook Documentation: Export detailed TSV or Markdown metadata tables listing panel IDs, image asset paths, acquisition notes, and scale bar lengths.

Scientific Background

Major scientific journals strictly enforce physical page column widths—such as Nature (89 mm single-column, 170 mm double-column), Cell (85 mm / 174 mm), and Science (55 mm / 175 mm)—to guarantee readable typography and figure legibility in print and PDF formats. Manual layout in general vector graphics editors often leads to improper width scaling, non-standard font sizes, distorted aspect ratios, or misaligned scale bars. Programmatic layout scaffolding computes panel widths ($W_{\text{panel}}$), gap spacing ($G$), and canvas heights based on explicit publisher constraints ($W_{\text{canvas}} = 2M + C \cdot W_{\text{panel}} + (C - 1)G$), ensuring layout compliance and structured metadata management prior to final graphic production.

Web Application

For researchers who prefer a graphical interface, an interactive web version is available.

Web Application: https://www.pepkio.com/tools/figure-panel-mockup-grid

Web-only features include interactive drag-and-drop grid creation, real-time column width guides, visual canvas rendering, shareable permalinks, and interactive asset manifest worksheets.

Documentation and Resources

GitHub Repository: https://github.com/pepkio/pepkio-figure-panel-mockup-grid

Web Application: https://www.pepkio.com/tools/figure-panel-mockup-grid

Source code and issue tracking are maintained on GitHub.

About Pepkio

Pepkio (https://www.pepkio.com/) develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services (https://www.pepkio.com/cro). Explore additional online laboratory calculators and workflow tools at https://www.pepkio.com.

Keywords

• scientific figure panel
• figure layout grid
• journal column width
• figure panel mockup
• publication figure
• multi-panel figure
• figure alignment
• Nature figure layout
• Cell figure layout
• Science figure layout
• PNAS figure layout
• Western blot layout
• microscopy figure grid
• scale bar annotation
• aspect ratio lock
• panel scaffolding
• figure inventory table
• figure metadata
• composite figure builder
• figure grid generator
• bioinformatic figure tool
• manuscript layout validator
• figure panel renumbering
• scientific illustration grid
• manuscript figure prep
• scientific figure grid generator
• journal compliant figure layout
• multi panel Western blot grid
• fluorescence microscopy panel layout
• publication column width validator
• automated figure panel alignment
• figure panel inventory export
• single column figure layout
• double column figure layout
• multi panel scientific illustration
• scientific figure layout planning
• Python client for scientific figures
• scientific figure panel scaffolding
• manuscript composite figure layout