Getting Started

Launching TomoGUI

Start TomoGUI from the command line:

tomogui

The main window opens ready to load a dataset.

TomoGUI main window on launch

TomoGUI main window with a dataset loaded. Left: controls and the parameter tabs. Right: reconstructed image with contrast and slice controls.

Basic Workflow

  1. Select Data Folder — click Browse Data Folder and navigate to your tomography data directory. HDF5 projection files in the folder appear in the Projection File dropdown (and in the Batch tab).

  2. Select Projection File — pick the .h5 file to reconstruct.

  3. Configure Reconstruction — reconstruction method, COR method, algorithm, binning, nsino-per-chunk, ring-removal, phase retrieval, etc.

  4. Try — click Try to run a quick multi-COR try reconstruction. The result appears under <folder>_rec/try_center/<dataset>/.

  5. View Try — switch to the try-center slice viewer and pick the best COR, or let AI Reco choose one automatically (see AI Reconstruction).

  6. Full — click Full to run the full reconstruction with the chosen COR.

Main tab with parameters filled in

Main tab with dataset selected and reconstruction parameters filled in.

Your First Reconstruction

1. Browse Data Folder      → /data2/32ID/2026-04-Allen-0/
2. Projection File         → sample_0001.h5
3. Reconstruction method   → recon
4. COR method              → manual
5. COR value               → 1024.5
6. GPU                     → 0
7. Click Try
8. Click View Try, pick the best slice
9. Click Full

After Try, the try-center grid can be previewed directly in the image panel and the COR slider on the right lets you scrub through candidate centers.

Understanding the Interface

Main Layout

The window is divided into two main panels:

Left Panel — controls and parameter tabs:

  • Main — Try / Full / AI Reco / TomoLog buttons and common parameters

  • Reconstruction — algorithm, nsino-per-chunk, binning, etc.

  • Hardening — beam hardening correction

  • Phase — phase retrieval parameters

  • Rings — ring artifact removal

  • Geometry — geometric corrections

  • Data — data preprocessing

  • Performance — performance tuning

  • Advanced Config — full configuration file editing

  • Batch — multi-file batch processing (see Batch Processing Guide)

  • HDF5 Viewer — inspect projections and metadata

Right Panel — visualisation:

  • matplotlib image display with toolbar

  • colormap controls

  • contrast (Auto 5–95 % / Reset / Min / Max)

  • slice / COR slider

  • TomoLog integration panel

Log Output

The log area shows:

  • command execution status

  • success / failure messages

  • processing progress

  • error information

  • per-file streaming during Batch AI Phase B

Status indicators use coloured text: green ✓ for success, red ✗ for failure, amber for warnings.

Next Steps