Reconstruction Workflow

This page covers the single-file reconstruction workflow. For multi-file operations, see Batch Processing Guide; for automatic COR discovery, see AI Reconstruction.

Quick reference

  1. Load data folder and select a file

  2. Set reconstruction parameters (COR, algorithm, binning, …)

  3. Run Try (or AI Reco) to pick a COR

  4. Evaluate the try output

  5. Adjust parameters if needed

  6. Run Full

Main tab with reconstruction parameters

Try vs Full

Try Reconstruction

  • Runs over a small slice range at multiple candidate CORs

  • Fast (seconds to a few minutes)

  • Output: <folder>_rec/try_center/<dataset>/center*.tiff

  • Used for: picking the COR, checking data quality, tuning filter params

Full Reconstruction

  • Processes the complete dataset

  • Slower (minutes to hours depending on size / binning)

  • Output: <folder>_rec/<dataset>/recon_*.tiff

Reconstruction Methods

TomoGUI exposes all TomoCuPy methods via the Recon tab:

FBP

Direct filtered backprojection. Fast, sufficient for most datasets.

gridrec

Grid-based FBP. Good quality / speed trade-off for 360° scans.

LPREC

Log-polar reconstruction. Faster for very large sinograms.

Additional flags (recon_steps vs recon, binning, nsino-per-chunk, start / end slice) are available on the same tab.

Centre of Rotation

COR can be set four ways:

  1. Manual — type a value in the COR field on the Main tab.

  2. Auto — TomoCuPy’s built-in auto-centre. Selected via the COR method dropdown.

  3. Try + View Try — run Try, slide through candidate CORs, pick the best one, it is copied into the COR field.

  4. AI Reco — DINOv2-based automatic selection (see AI Reconstruction). Result is written to <folder>_rec/try_center/<dataset>/center_of_rotation.txt and pulled back into the GUI.

For multi-file operations, see COR Management for how per-row CORs interact with the top-bar COR input, and how Fix COR Outliers works.

Output folders

All output lives next to the data folder with a _rec suffix:

/data/tomo/scan/                    ← projections
/data/tomo/scan_rec/                ← reconstructions
    ├── try_center/<dataset>/        ← try TIFFs + center_of_rotation.txt
    └── <dataset>/recon_*.tiff       ← full reconstruction

Per-dataset parameters

Every reconstruction parameter tab writes its values to a JSON sidecar next to the projection file. Re-loading the file restores its last-used parameters. This sidecar is also what the Batch tab reads when you click Apply parameters to selected on a row.