Cengraph features an intuitive, high-density dark workspace engineered specifically for scientific spectroscopy. The interface consists of five core regions: Main Menu Bar, Data Explorer Panel (left), Vector Canvas Engine (center), Analysis & Style Inspector (right), and Real-Time Coordinates Toolbar (bottom).

1. Launch Cengraph to load your persistent dark workspace preset (#09090B deep obsidian background).
2. Toggle sidebars using Ctrl + B (Data Explorer) or Ctrl + Shift + I (Inspector) to maximize plot canvas area.
3. Drag panel divider splitters to resize tree views, spectrum lists, and spectrum inspection properties.
4. Use the Top Toolbar for quick access to peak inspection, pan/zoom, vector annotation, and figure export tools.

Cengraph features a universal multi-vendor file reader that automatically parses raw spectroscopic files from Renishaw, Horiba, Thermo Fisher, Bruker, Ocean Optics, and custom laboratory instruments.

1. Click File > Open Data or press Ctrl + O. Alternatively, drag and drop files onto the active canvas.
2. Supported file extensions include .txt, .csv, .wdf (Renishaw), .labspec (Horiba), and .dat.
3. In the Import Dialog, Cengraph automatically detects delimiters (Tab, Comma, Space, Semicolon) and header text offsets.
4. Enable “Auto-Group by Prefix/Directory” to group multi-sample spectral series into unified color-coded datasets.

Cengraph utilizes .cgph (Cengraph Project History), a native high-performance binary session archive that preserves raw data, baseline models, fitted peaks, canvas annotations, and custom theme presets without analytical precision loss.

1. Save your workspace session by clicking File > Save Project (.cgph) or pressing Ctrl + S.
2. Access recent projects directly from the Start Hub welcome screen or File > Recent Projects.
3. .cgph archives store full 64-bit floating-point spectral data without truncation, preserving exact baseline and peak fits.
4. Automatic session locking protects against duplicate open windows and accidental file overwrites across desktop sessions.

Background fluorescence and matrix interference are automatically removed using the Whittaker-Eilers Asymmetric Least Squares (AsLS) baseline estimation algorithm.

1. Select target spectrum and open Analysis > Baseline Correction > AsLS or press Ctrl + Shift + B.
2. Adjust Smoothness Penalty (λ): Higher values (e.g., 10⁵ – 10⁷) generate stiffer, smoother baselines; lower values follow minor curvature.
3. Adjust Asymmetry Factor (p): Values between 0.001 and 0.05 ensure baseline strictly bounds signal troughs without clipping peak tops.
4. View real-time baseline preview superimposed on your spectrum before clicking Apply Subtraction.

Savitzky-Golay filtering removes high-frequency experimental noise using localized polynomial least-squares regression, preserving peak amplitude, location, and spectral linewidths.

1. Open Analysis > Noise Reduction > Savitzky-Golay or press Ctrl + Shift + G.
2. Set Polynomial Order (k): Typically set to 2 or 3 to preserve peak shape without over-fitting noise.
3. Set Frame Window Size (m): Must be an odd number (e.g., 7, 11, 15, 21 points). Broader windows increase smoothing strength.
4. Select Derivative Order: 0 for standard smoothing, 1st Derivative for slope analysis, or 2nd Derivative for resolving overlapping doublet peaks.

Standardize intensity scales across varying sample thicknesses, laser powers, and acquisition integration times for accurate sample-to-sample comparison.

1. Highlight single or multiple spectra in the Data Explorer list.
2. Navigate to Analysis > Normalization or press Ctrl + Shift + N.
3. Select from four scientific normalization algorithms:
   • Min-Max [0, 1]: Rescales intensity so minimum is 0 and peak maximum is 1.0.
   • Vector / Euclidean Norm: Divides intensity vector by its L2 norm (√∑Y² = 1).
   • SNV (Standard Normal Variate): Subtracts mean and divides by standard deviation (μ=0, σ=1).
   • Peak Area Normalization: Normalizes total integrated spectral area under curve to 1.0.
4. Click Apply Normalization to update all selected plot traces simultaneously.

Design publication-ready multi-figure layouts with independent or linked axes, stacked waterfall displays, and multi-panel comparison matrices within a single workspace.

1. Click Canvas > Add Artboard or press Ctrl + Shift + A.
2. Select layout arrangement: Single Artboard, Stacked Vertical (Waterfall), 2×2 Grid, or Multi-Panel Row.
3. Drag spectra from the Data Explorer onto specific artboard subpanels.
4. Toggle Synchronize X-Axis Zoom to navigate wavenumber ranges across all subpanels simultaneously.

Cengraph legend boxes are fully interactive vector components that can be placed anywhere on the canvas with drag-and-drop precision and styled to match journal requirements.

1. Click and drag the legend box anywhere across your active vector artboard.
2. Double-click the legend to open the Legend Property Editor dialog.
3. Customize legend title, sample label names, line stroke swatches, font size, and background opacity.
4. Toggle legend border line, shadow blur, or transparent glassmorphic background fill.

Add publication-quality callouts, peak indicators, chemical formulas, structural arrows, and LaTeX math typography directly onto the vector plot layer.

1. Select an annotation tool from the top toolbar: Peak Callout, Vertical Marker Line, Arrow, Rectangle, or LaTeX Text.
2. Click on a specific spectral peak to anchor the annotation directly to data coordinates (Wavenumber, Intensity).
3. Double-click text box to enter labels with integrated LaTeX formatting (e.g., $\nu_{1}(A_{1g})$ or $\text{cm}^{-1}$).
4. Customize line dash styles (Solid, Dashed, Dotted), arrow head styles, and color accents in the Style Inspector.

Fit complex overlapping spectral envelopes using non-linear least-squares peak deconvolution with Gaussian, Lorentzian, and Voigt band profiles.

1. Highlight region of interest on your spectrum using Shift + Click & Drag.
2. Open Analysis > Peak Analyzer / Deconvolution or press Ctrl + Shift + P.
3. Click Auto-Detect Peaks or double-click peak maxima to position initial peak seeds.
4. Choose line shape profile (Gaussian, Lorentzian, or Pseudo-Voigt) and click Run Deconvolution.

Generate ultra-high resolution vector and raster figures customized to target journal publisher standards (Nature, ACS, RSC, Elsevier, Wiley).

1. Click File > Export Figure or press Ctrl + E.
2. Select output format:
   • SVG: Scalable Vector Graphics for Adobe Illustrator / Inkscape editing.
   • PDF: Vector PDF with embedded fonts for direct manuscript submission.
   • PNG / TIFF: High-density raster images at 300, 600, or 1200 DPI.
3. Choose publication physical dimension preset: Single Column (89 mm) or Double Column (183 mm).
4. Click Export Figure to render your publication-ready graphic instantly.

Maximize laboratory workflow speed with multi-tab project navigation and comprehensive zero-mouse hotkey shortcuts.

1. Work on multiple active spectral projects simultaneously across tabbed project views.
2. Switch tabs using Ctrl + Tab or Ctrl + Shift + Tab.
3. Memorize core hotkeys for data loading, processing, baseline fitting, and figure export.
4. Customize shortcut mappings via Preferences > Keyboard Shortcuts.