Thesis Figures with SciDAVis: From Plot to Printed Page

A thesis stands or falls on its figures — examiners notice blurry axes, mismatched fonts, and inconsistent styles long before they notice your statistics. This guide is a workflow, not a button-by-button manual: how to get a graph out of SciDAVis, into your Word document or LaTeX thesis, and polished to submission standard with free tools. The mechanics of the export dialog itself are covered in the companion guide Export Publication-Quality Figures (SVG, EPS, PDF); read that first if you haven’t exported anything yet.

The thesis figure pipeline

Do these five steps in order, for every figure, and your thesis will look like one coherent document instead of a scrapbook:

1. Plot and style in SciDAVis. Final axis labels, units, fonts, and legend — before exporting.
2. Export a vector master (SVG, PDF, or EPS). This is your archival copy.
3. Insert into your document: PNG for Word, PDF for LaTeX.
4. Polish in Inkscape — cosmetic fixes only (label nudges, panel letters, alignment).
5. Archive the SciDAVis project (.sciprj) alongside the figure, so you can regenerate it when an examiner asks for a change.

Step 1 — Choose your formats before you plot, not after

The single most common mistake is plotting first and choosing a format last. Decide now:

Rule of thumb: if your figure is lines, symbols, and text — which is nearly everything SciDAVis produces — a vector format is always the right master. Bitmaps are only the final step for Word.

Step 2 — Style the graph for print while it’s still in SciDAVis

Export captures the graph window as it is, so fix these before you touch the Export dialog:

• Size the window to the final figure size. A single-column figure is typically 8–9 cm wide; a full-page figure about 17 cm. If the window is much larger than its target, text and line widths will look wrong after scaling.
• Use thesis-matching fonts. Pick the same family your thesis template uses (a standard serif for body-matching figures, a common sans-serif for slides). SciDAVis embeds font names, not the fonts themselves — stick to fonts that will exist on the machine that renders the final PDF.
• Label axes with units (“Time (s)”, “Absorbance (a.u.)”), and keep the legend inside the plot frame where possible so nothing gets clipped.
• One style per thesis. Same tick length, same line widths, same color palette on every figure. Save your styling as a reusable template with File → Save as Template — the plot templates guide shows how.

Step 3a — The Microsoft Word route: PNG, high resolution, no compression

Word and vector graphics have an uneasy relationship, so for Word theses the reliable path is a high-resolution PNG:

1. In SciDAVis, open the Export Graph dialog and export a PNG at 300 dpi or higher (600 dpi for a full-page figure is safer).
2. In Word, use Insert → Pictures → This Device — never drag-and-drop from a browser, which can silently downscale.
3. Turn off Word’s automatic image compression, or it will undo your careful 300-dpi export: File → Options → Advanced → Image Size and Quality, tick “Do not compress images in file”, and set the default resolution to High fidelity.
4. Size the image with the corner handle (hold Shift to keep proportions); never stretch it wider than its exported resolution.

Step 3b — The LaTeX route: PDF figures, one line each

This is the cleaner route. Export the graph as PDF from SciDAVis, drop the file next to your .tex sources, and include it with:

\begin{figure}[htbp]
  \centering
  \includegraphics[width=\columnwidth]{fig3-kinetics.pdf}
  \caption{First-order rate plot for the reaction at 298\,K. Error bars show the standard deviation of three replicates.}
  \label{fig:kinetics}
\end{figure}

Notes that save hours of debugging:

• pdfLaTeX embeds PDF figures natively — no conversion step, no quality loss.
• If your template is an older one that demands EPS (some university classes still do), export EPS from SciDAVis and convert with epstopdf; the result is identical for plotting purposes.
• Set width=\columnwidth (or 0.8\columnwidth) rather than a fixed size, so the figure follows your template’s margins automatically.

Step 4 — Polish in Inkscape (cosmetic fixes only)

Even a well-styled SciDAVis graph occasionally needs a nudge: a panel letter here, a re-aligned legend there, two related figures merged side by side. Inkscape (free, open-source) opens SciDAVis SVG exports as fully editable vector objects:

1. File → Open the SVG master in Inkscape.
2. Nudge labels, add panel letters like (a) and (b), align multi-panel composites with the Align tools.
3. Export the finished composite as PDF (for LaTeX) or PNG (for Word).

This SciDAVis → Inkscape → (GIMP for photos) chain is exactly what several university lab courses teach for publication-quality figures — including the Kilgour Lab’s open teaching materials on making figures with free software. One ethical boundary to respect: polish, don’t redraw. Moving a label is fine; moving a data point is fabrication. Keep every edit cosmetic.

Pre-submission figure checklist

• Every figure is vector (or 300+ dpi raster) — no screenshots of your own plots.
• Fonts are consistent across all figures and match the thesis template.
• All axes labeled with quantities and units; no default “Column 1” labels anywhere.
• Captions describe what the reader should conclude, not just what is plotted.
• Colors are distinguishable in grayscale (print your thesis draft in black and white once — many examiners still do).
• Figure files are named consistently (fig3-kinetics.pdf, not untitled_export2_final_v3.png).