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How to measure lesions on CT or MR and export a PDF or CSV report with Voxenra

Draw length, angle and ROI measurements on images, then export the results as CSV, PDF or DICOM SR.

Who it is forA clinical researcher or radiologist who needs written measurements from a study for a case review or a research record.

The problemMeasurements scattered across viewer screenshots are hard to reproduce and hard to share.

The outcomeA list of measurements with area, perimeter and intensity statistics, exported as CSV or PDF with a matched reference image, or as DICOM SR.

What you need first

  • Python with uv installed, so the README command `uv run voxenra` works
  • Local DICOM, NRRD or PACS-accessible CT, MR or PET/CT data you are allowed to use
  • For AI auto-segmentation: a separately installed TotalSegmentator environment and CT fast model, detected under Settings → AI
  • A desktop OS: macOS Apple Silicon or Windows x64 release builds are listed, or a source checkout run with uv

Steps

  1. Clone the repo from https://github.com/l5769389/voxenra and enter the folder.
  2. Run uv run voxenra and import the study by file, folder, archive or PACS query.
  3. Open the series in two-dimensional view and draw length, angle, curve or ROI measurements.
  4. Check each measurement in the list, rename or lock items, and fix any mistakes with undo.
  5. Export the results as CSV, PDF or DICOM SR from the measurement export options.

Prompt for your agent

Work in the repo l5769389/voxenra. Start it with `uv run voxenra`, open <path to study>, and measure the lesion with a length tool. Export the results to <output folder> as CSV and confirm the file lists each measurement with its value.

Caveat. Physical size measurements need valid pixel spacing in the image data, and the README says HU analysis is not available for colour images.

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