UX Research + Design · UT Austin · Fall 2024
Reimagining
PyReconstruct
Enhance the usability of PyReconstruct for lab researchers in order to have an easy and efficient experience?
00 — Context
What is PyReconstruct?
PyReconstruct is a neuroscience tool used by researchers at UT Austin to trace, annotate, and reconstruct 3D models of brain synapses from electron microscopy images. It's a critical daily-use research tool — yet had a SUS score of 67.5, firmly in the "Grade D" range.
Our team of five designers partnered with the PyReconstruct development team to identify usability barriers and design targeted improvements — working directly with the developers and a professor who oversaw real lab usage.
01 — The Problem
A tool researchers had to be taught in person
A heuristic evaluation and accessibility audit revealed 20+ usability violations. New users had no choice but to learn the app through one-on-one training — there was nothing inside the app to guide them.
Four critical failures
- No onboarding whatsoever. Beginners were taught one-on-one by experts. No tour, no tooltips, no help text on first launch.
- 20 unlabeled icons, no grouping. Two rows of identical-looking shapes. Users couldn't tell trace from stamp — no hover states, no labels.
- Broken critical workflows. Bug reporting required leaving to GitHub. 3D view took 4 menu clicks. Undo had no visible button.
- 6+ WCAG AA failures. Failed contrast, hover states, error messaging, orientation, and sensory characteristics.
Evidence from heuristic evaluation
02 — Research
Two very different users, one shared frustration
We conducted in-depth interviews with expert and beginner users. Despite their different skill levels, both hit the same wall — the interface gave them nothing to work with.
Primary Persona
The Expert
Pain Points
- Interface uses 50% of screen
- Shortcuts not visible anywhere
- Default settings change unexpectedly
Goals
- Automate and analyse data
- Keyboard-first workflow
- Accessible, modern UI
Secondary Persona
The Beginner
Pain Points
- No welcome tour or guidance
- Can't distinguish icons
- No system status feedback
Goals
- Finish tasks independently
- Align 100s of sections
- Work confidently in 3D
What we heard
"The interface uses 50% of my screen — it's just frustrating."Expert user
"I cannot remember any keyboard shortcuts."Beginner user
"Very clean." — First reaction to the redesign.Beginner user
03 — Priority
20+ issues. One led the brief.
Every finding was mapped on a severity × impact matrix. Onboarding topped the list — it affected every user, expert and beginner alike. Without fixing it, everything else was secondary.
Onboarding + Welcome Tour
Zero guidance for first-time users — learned only by word of mouth
Confusing Navigation (IA)
Nav labels didn't match mental models — restructured via card sorting
Trace & Stamp Tool Clarity
Users couldn't distinguish open/closed trace or stamp function
In-App Bug Reporting
Required leaving to GitHub — broke every workflow
3D View Access
4-click menu navigation to a feature used regularly
WCAG Contrast + Error Messages
6+ AA failures across the interface
04 — Solution
Designing the onboarding that never existed
We designed a 12-step welcome tour, a new entry screen, and restructured navigation — each solution directly tied to a research finding. Three rounds of user testing shaped the final designs.
A welcome screen for first-time users
The original app launched straight into a black screen. We introduced a clear welcome page with two distinct paths: Get Started and Take a Tour.
A 12-step tooltip tour
Tooltips appear exactly where users need to act, inside the real interface. Each tooltip is one sentence, always shows the keyboard shortcut, and avoids jargon.
Before vs. after: a user's first day
Before
- Open app → black screen, no guidance
- Find a colleague to show you around
- Ask how to import an image series
- Ask what the knife tool does
- Ask how to access 3D view
- Still unsure about shortcuts weeks later
After
- Welcome screen — Get Started or Take a Tour
- Tour step 1 — Import and define assets (⌘N)
- Knife tool explained inline, step 3
- Covers trace, stamp, 3D access, shortcuts
- Links to Help resources & searchable shortcuts
- Ends with confetti — tour complete
The final redesigned interface
Restructured navigation from card sorting, labelled toolbar icons with hover states, and a 3D cube accessible in one click from the toolbar.
05 — Outcomes
Measurable improvements, handed off
We delivered Figma assets, a WCAG accessibility guide, and 20+ design recommendations directly to the PyReconstruct development team.
Team
Srilalitha · Ishita · Manasi · Deep · M. Chirillo (PyReconstruct) · M. McQuaid (Professor)
INF 385T · UX Prototyping · University of Texas at Austin · Fall 2024
