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Changelog

All notable changes to Dioptra. Versions follow semantic versioning; the file format has its own version (see the manual’s File format chapter).

0.4.0 — 2026-10-14

Prism files both ways, plate readers, and Dioptra Lab.

Free

  • Prism import reads .prism files (Prism 10 and later) as well as .pzfx. Nested and multiple-variables tables keep their kind; subcolumn titles are kept; CV, low–high and limits formats are converted, with a note; calendar dates become row titles. Tested on 53 real Prism files from Prism 6 to 11.
  • Plate-reader import: SoftMax Pro (.txt), BMG MARS (CSV), Agilent BioTek Gen5 (.txt) and Tecan Magellan (.xlsx), endpoint and kinetic, with an optional plate map of wells to groups and doses. File → Import file… recognises them by content.
  • Replace table data… loads a new file into an existing table and keeps its formulas, analyses and graphs.
  • Verify records: the audit trail and signatures of a regulated project can be checked, viewed and exported without a license.
  • Fixed outlines (0.4–0.6 pt) now follow the graph’s line width.

Dioptra Lab

A yearly license for labs, core facilities and regulated groups; see the pricing page. Keys are checked on the computer; nothing is sent anywhere. Help → Dioptra Lab… takes the key.

  • Batch analysis: apply a project as a template to many data files, with a summary table and figures per file; a watch folder for instrument exports; dioptra batch.
  • Journal figures: presets for nine journals, a figure check (text size, line width, resolution, colours colour-blind readers cannot tell apart, mismatched panels), TIFF export, layouts at final size with panel letters, a methods paragraph, and a Word or PDF report of the project.
  • Prism export: File → Export to Prism… writes data tables as .pzfx; dioptra convert converts folders in either direction.
  • Records for regulated labs: users and roles, a hash-chained audit trail with reasons, electronic signatures that lock a record, and a validation pack (compliance matrix, traceability, IQ/OQ protocols) with an automated OQ of 8,212 checks (Records → Run OQ…, dioptra oq).

File format

dioptra/1.2: layouts gain style; files may carry extensions/<name>. Dioptra 0.3 opens 1.2 files.

Command line

dioptra batch, dioptra convert, dioptra oq, dioptra license.

0.3.0 — 2026-10-12

Connecting lines: Prism’s before–after graphs, made an option of every bar graph.

Graphs

  • Connecting lines on column, strip, box and violin graphs (options.connecting): a line per subject joining the values of each row across the bars, the means or medians joined across the bars, or both. Lines are drawn above bars, boxes and violins and beneath the points; the summary line on top. Style (solid, dashed, dotted), width, opacity and colour: one colour, by data set, per subject from a palette, or by a grouping column with a legend. A missing value leaves a gap (or the line joins across it). On grouped tables the lines run within each group across its data sets (matched subcolumns) or along each data set across the groups. With jitter on, each line ends at its own jittered point. Lines are cut where they cross an axis break. Every subject line is a target in the graph editor.
  • Paired t, ratio paired t, Wilcoxon, repeated-measures ANOVA and Friedman now graph as bars with connecting lines; the results sheet’s button says Graph with connecting lines. The New graph dialog offers Bars with connecting lines and Before–after (points) as presets for column and grouped tables.
  • Horizontal column, strip, box and violin graphs (options.orientation); axes.y stays the value axis, as in Prism.
  • Bar options from a comparison with Prism’s Format Graph: error-bar direction (both, above, below) and cap width; bar width and slot width (the gaps between bars and between groups); bar fill (tint, solid, outline); fill patterns per data set (diagonals, crosshatch, horizontal, vertical, dots), drawn as geometry so SVG, PDF and PNG agree; strip graphs without points (mean ± error only) or without the mean line.
  • Open markers (circle_open and friends) now draw open on column graphs.
  • Any line now breaks where it crosses an axis break, and horizontal bars are cut at breaks of the value axis.
  • New inspector sections: Connecting lines and Bars and points (orientation, summary, jitter, fill, widths, error-bar direction and caps); a pattern control per data set.

File format

  • Format 1.1. Graph specs gain the fields above; defaults are not written, so graphs without them are saved as before. The before_after family is retired: opening a 1.0 file turns such graphs into the strip spec that draws the same picture (unjittered points, subject lines, the mean line when it was on). docs/FILE-FORMAT.md documents the migration.

Research and docs

  • research/06-connecting-lines.md: what Prism’s column, grouped and categorical graphs offer for connecting lines, with sources, and how Dioptra maps each option.
  • Manual: Connecting lines and paired graphs, with a worked example.

0.2.1 — 2026-10-12

Fixed

  • macOS: the app opened as “Dioptra is damaged and can’t be opened”. The bundle is now ad-hoc signed as a whole (bundle.macOS.signingIdentity: "-"), and the release job fails unless codesign --verify --deep --strict passes on the .app inside the .dmg. The app is still not notarized: the first launch needs right-click → Open (macOS 15 and later: Privacy & Security → Open Anyway) or xattr -cr /Applications/Dioptra.app. See docs/macos-gatekeeper.md.

0.2.0 — 2026-10-12

The design release: the same engine, a redesigned instrument.

Interface

  • A design system (DESIGN.md §12): warm paper neutrals in light, deep graphite in dark, one verdigris accent, Inter for the interface and JetBrains Mono with tabular figures for every number, an 8-pt spacing scale, Lucide icons, designed focus rings and thin themed scrollbars. Every text/background pair meets WCAG AA in both themes (docs/DESIGN-AUDIT.md, scripts/contrast.mjs).
  • No native form control anywhere: own Select, Segmented, Toggle, Checkbox, NumberField with unit suffixes, ColorSwatch, Menu, Dialog and Tooltip.
  • The in-window menu bar is gone. A slim top bar carries the mark, the project title (click to rename), the command field and the theme control; the menu tree lives in a compact Menu popover and the command palette. macOS gets a native system menu.
  • Dark mode follows the operating system (and the Tauri window theme) by default, with a light/dark/system control in the top bar, View and the palette; every surface is designed for dark rather than inverted.
  • The grid is a bounded sheet: rows end where the data ends plus a margin, with “+ rows” and “+ Data set” affordances; data-set headers carry a kind glyph and the colour swatch the graph will use; a designed selection with corner handles; comfortable and compact density; a first-class formula bar; human-readable provenance times.
  • Results sheets in a reading column with the type system, hairline tables, mono numbers, assumption cards with designed marks and the alternative on a second line.
  • The graph editor is a desk with millimetre rulers, a paper choice (white, theme, transparent), a designed zoom control, hover halos and a selection frame on targets, and collapsible inspector sections that remember their state.
  • A designed first launch: paste data, open the bundled sample project, or read the manual.
  • A new icon set from the dioptra mark; window size, position and panel widths are remembered.
  • The paste dialog’s segmented choices sit at their own width instead of stretching across the column.
  • A designed README banner (also the landing page’s Open Graph image), and a landing page whose captures follow its light or dark theme.

Engine

  • SetProjectTitle command (undoable); the risk-difference Wald interval is clamped to [-1, 1].

0.1.0 — 2026-10-11

The first public release.

Data tables

  • Eight table kinds: XY, Column, Grouped, Contingency, Survival, Parts of whole, Multiple variables and Nested, each explained with a sketch when a table is created.
  • Subcolumn formats: replicate values, mean/SD/N, mean/SEM/N, mean/CI/N, mean/SD, mean/SEM, median/IQR, lower/upper and single values.
  • A virtualised grid that holds a million cells, with the full spreadsheet keyboard set, fill down, undo and redo across every action, and a status line with n, mean, SD and sum.
  • Text cells kept as text, never coerced; excluded values struck through and kept.
  • Cell provenance: typed, pasted (with time), imported (file, sheet, column), formula or derived, plus a per-cell edit log.

Getting data in and out

  • Paste with automatic separator, decimal-comma and header detection, and a report of what was decided; ambiguous values such as 1,234 are kept as text and reported.
  • Paste as a new table with a suggested table kind.
  • Import of CSV, TSV, text, XLSX, XLS, ODS (built-in reader, stored values at full precision) and Prism .pzfx data tables.
  • Export of tables to CSV, TSV and XLSX.

Formulas and transforms

  • Column formulas and cell formulas with fill-down, a dependency graph, pull-based recomputation and circular-reference detection.
  • Arithmetic, logic, row functions, summaries, series functions (lag, lead, diff, cumsum, rank, zscore, baseline), slices, and unit conversion including mass-to-molar conversion for glucose, cholesterol, triglycerides, creatinine and urea.
  • Derived tables with stored recipes: transpose, pivot long to wide and wide to long, stack, filter, sort, select rows and columns, remove baseline, fraction of total, normalise, average replicates and prune.

Command line

  • dioptra info, run, import, analyze, render, export, bench and equations drive the same engine from scripts and continuous integration.

Analyses

  • Twenty analyses: descriptive statistics; t tests (one-sample, Welch, Student, paired, ratio paired); Mann–Whitney; Wilcoxon signed-rank; one-way ANOVA with Welch and Brown–Forsythe; repeated-measures one-way ANOVA with Greenhouse–Geisser and Huynh–Feldt; two-way ANOVA (types I, II, III; one repeated factor); Kruskal–Wallis; Friedman; chi-square; Fisher’s exact test (2 × 2 and r × c); correlation (Pearson, Spearman, Kendall); simple linear regression with bands and diagnostics; nonlinear regression; normality tests; outlier identification (Grubbs, ROUT); survival (Kaplan–Meier, log-rank, Gehan–Breslow–Wilcoxon, hazard ratios); ROC curves; Bland–Altman; principal component analysis.
  • Multiple comparisons: Tukey–Kramer, Dunnett, Šidák, Holm, Bonferroni, Dunn and Benjamini–Hochberg.
  • Nonlinear regression with the equation library (4PL, 5PL, exponential, Michaelis–Menten, Hill, binding, Gaussian, polynomials and more), custom equations, weighting, robust fitting, constraints, shared parameters, profile-likelihood intervals, model comparison by extra sum of squares and AICc, and ROUT.
  • Results sheets with assumption checks shown first, APA-style summary sentences, a methods sentence, effect sizes with confidence intervals, and a reporting checklist.
  • P-value styles APA (default), NEJM, GP and exact, applied project-wide.
  • Analyses listed by fit to the table, with the reason for each that does not fit.

Graphs

  • Twenty-three families: scatter, line, column, box, violin, strip, raincloud, before–after, estimation, SuperPlot, histogram, density, heatmap, correlation matrix, Kaplan–Meier with at-risk table, ROC, Bland–Altman, volcano, forest, pie, donut, QQ and residual plots; column graphs can be grouped, stacked or percent-stacked.
  • An interactive editor: click any element to edit it in the inspector, drag the legend and annotations, edit text in place; significance brackets, reference lines and labels.
  • Themes Instrument, Night and Journal; palettes Okabe–Ito (default), Tol bright, muted and light, viridis, cividis, Tol sunset and grey.
  • Sizes in millimetres, type and lines in points, journal presets; multi-panel layouts with panel letters.
  • Export to SVG (real text), PDF (embedded subset fonts) and PNG at any resolution; identical bytes on every platform.

Files and reproducibility

  • The .dioptra project file: a zip of documented, pretty-printed JSON with the data, formulas, analysis and graph specifications, and the command history.

Correctness and performance

  • All 58 NIST StRD data sets used (univariate, linear regression, ANOVA, nonlinear regression) pass; 7,841 comparisons against SciPy, statsmodels, lifelines and scikit-learn agree within tolerance.
  • A million-cell paste in about 0.13 s; a column formula over a million rows in under 0.11 s.

Platforms

  • Linux (AppImage, deb, rpm), Windows (msi, setup exe) and macOS (Apple silicon and Intel dmg), built from one codebase.