Interface Overview

TomoGUI is split into a left-hand control panel (parameters, tabs, log) and a right-hand visualisation area (image, contrast, slice controls).

TomoGUI main window

TomoGUI main window.

Main Window Layout

┌─────────────────────────────────────────────────────────┐
│ TomoGUI                                         🌙 / ☀   │
├──────────────────┬──────────────────────────────────────┤
│                  │                                      │
│  Control Panel   │     Visualisation Area              │
│  (Left)          │     (Right)                         │
│                  │                                      │
│  Data Folder     │  Matplotlib canvas                  │
│  Projection File │  Navigation toolbar                 │
│                  │  Colormap, Contrast, Auto-5/95 %    │
│  Tabs            │  Slice / COR slider                 │
│   • Main         │  TomoLog panel                      │
│   • Recon        │                                      │
│   • Hardening    │                                      │
│   • Phase        │                                      │
│   • Rings        │                                      │
│   • Geometry     │                                      │
│   • Data         │                                      │
│   • Performance  │                                      │
│   • Advanced Cfg │                                      │
│   • Batch        │                                      │
│   • HDF5 Viewer  │                                      │
│                  │                                      │
│  Log Output      │                                      │
│                  │                                      │
└──────────────────┴──────────────────────────────────────┘

Top tab bar

Top tab bar

The tab bar switches between:

  • Main — single-file and batch workflow in one view (Try, Full, AI Reco, TomoLog controls plus the file/batch table with Fix COR Outliers and Delete Selected)

  • Reconstruction / Hardening / Phase / Rings / Geometry / Data / Performance — per-category TomoCuPy parameter tabs

  • Advanced Config — remote host, GPU count, AI model path, extra flags

Left Panel

Data Selection

At the top of the left panel:

Data Folder

  • Current data directory

  • Browse Data Folder button

  • Path is persisted between sessions

Projection File

  • Dropdown of .h5 files in the folder, newest first

  • Refresh button reloads the list

Sync Acquisition

  • Automatically refreshes the dropdown as new files appear in the acquisition folder (useful during a live scan)

Data folder and file picker

Tab System

Main Tab

Main tab

Single-file workflow:

  • Try / Full — reconstruction controls (see Reconstruction Workflow)

  • AI Reco — DINOv2 automatic COR (see AI Reconstruction)

  • TomoLog — PDF report generator with per-file auto-contrast

  • View Try / View Full — quick access to the reconstructed output

Reconstruction Parameters Tabs

Per-category tabs below the Main tab expose every TomoCuPy flag:

  • Recon — algorithm (FBP, gridrec, LPREC), binning, nsino-per-chunk, start / end slice, etc.

  • Hardening — beam hardening correction

  • Phase — phase retrieval (alpha, energy, distance, …)

  • Rings — ring removal (sigma, level, algorithm)

  • Geometry — rotation axis geometry

  • Data — projection range, flat/dark correction

  • Performance — nthreads, blocked_views, etc.

Settings are stored per dataset in a JSON sidecar so reloading a file restores its last-used parameters.

Advanced Config Tab

Advanced Config tab

Cross-cutting configuration:

  • Remote host — SSH user@host for running reconstruction on a remote GPU node

  • Number of GPUs — parallelism for every batch phase (one file per GPU slot, next dispatched on slot free)

  • AI model path — absolute path to the .pth checkpoint

  • Extra flags — free-form extra command-line flags appended to tomocupy invocations

Batch table (on the Main tab)

See Batch Processing Guide for the full batch workflow. Key controls:

Batch file table

  • file table with per-row checkbox, COR, status, and series tint

  • Batch Try, Batch Full, Batch AI Reco, → TomoLog (optional Phase D upload)

  • Fix COR Outliers (also fills missing CORs from series mean), with Max COR delta (default 50 px)

  • Delete Selected (with confirmation)

  • Shift-click range selection

HDF5 Viewer

HDF5 Viewer

Right-click a row → View Data to open the HDF5 viewer on that file — browse the group tree, scrub through projections, check metadata.

Right Panel

Image display

  • matplotlib canvas with navigation toolbar (pan, zoom, save)

  • colormap selector (gray, viridis, magma, …)

  • Contrast — Min / Max inputs, Auto (5 – 95 % percentile), Reset

  • Slice / COR slider — when viewing a try-center grid, the slider scrubs through candidate CORs; when viewing a Full reconstruction, the slider scrubs through slices.

The auto-contrast behaviour also applies to TomoLog when Min/Max are blank.

Log Output

Structured log with colour-coded statuses:

  • ✓ success (green)

  • ✗ failure (red)

  • ⚠ warning (amber)

  • 🚀 job start

During Batch AI Phase B, per-file lines like [infer-worker] OK /data/.../sample_007.h5 => 1024.3 stream live and the corresponding COR cell updates in real time.