SyGlass Import/Export Pipeline

A collection of Python scripts for converting NIfTI data into SyGlass-compatible formats, creating SyGlass projects, importing masks and point annotations, and exporting data back out of SyGlass.

Workflow

NIfTI Volume (.nii.gz)
        ↓
convert_nifti_to_tiff.py
        ↓
TIFF Stack
        ↓
creating_project.py
        ↓
SyGlass Project (.syg)

NIfTI Mask (.nii.gz)
        ↓
convert_mask_to_tiff.py
        ↓
Mask TIFF Stack
        ↓
import_mask_in_syglass.py
        ↓
SyGlass Mask (.syk)

SPIMquant regionpropstats.tsv
        ↓
import_points.py
        ↓
SyGlass Counting Points

SyGlass Project
        ↓
export_mask.py
        ↓
Mask TIFF

SyGlass Project
        ↓
export_points.py
        ↓
Points TSV

Scripts

Script	Purpose
convert_nifti_to_tiff.py	Converts volumetric NIfTI images into TIFF slices for SyGlass project creation
convert_mask_to_tiff.py	Converts NIfTI segmentation masks into TIFF slices
creating_project.py	Creates a SyGlass project from a TIFF stack
import_mask_in_syglass.py	Imports a segmentation mask into a SyGlass project
import_points.py	Imports point detections from a SPIMquant regionpropstats.tsv file
export_mask.py	Exports the current segmentation mask from SyGlass
export_points.py	Exports counting points from SyGlass to TSV

Notes

• Mask imports require conversion from UINT8 to UINT16 prior to import.
• Point coordinates from SPIMquant must be converted from physical units to SyGlass voxel coordinates.
• Counting points are stored and retrieved using the SyGlass Python API.
• Segmentation export uses MaskOctreeRasterExtractor.

Status

✅ Create SyGlass project

✅ Import segmentation masks

✅ Import point annotations

✅ Export segmentation masks

✅ Export point annotations