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Multiscale analysis of the adult human superior hypogastric plexus and hypogastric nerve.

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Python · 236 lines · 7.7 KB · CC-BY-NC-4.0

  1. #!/usr/bin/env python3
  2. # SPDX-License-Identifier: CC-BY-NC-4.0
  3. # Copyright (c) 2026 Ziying (Alicia) Yang and contributors
  4. """Export raw image slices and mask slices from a syGlass project.
  6. The script reads a syGlass ``.syg`` project in Z chunks and writes:
  8. * one TIFF file per raw-image channel per Z slice
  9. * one TIFF mask-label file per Z slice
  11. Default outputs are written to ``raw_images`` and ``masks``. The workflow is
  12. chunked along Z to avoid loading the full 3D image volume into memory.
  13. """
  15. from __future__ import annotations
  17. import argparse
  18. import logging
  19. from pathlib import Path
  20. from typing import Optional, Sequence, Tuple
  22. import numpy as np
  23. import tifffile
  24. from tqdm import tqdm
  26. try:
  27. import syglass as sy
  28. from syglass import pyglass
  29. except ImportError as exc: # pragma: no cover - requires a local syGlass install
  30. raise ImportError(
  31. "Could not import the syGlass Python package. Install or activate the "
  32. "Python environment supplied with your syGlass installation before "
  33. "running this script."
  34. ) from exc
  36. LOGGER = logging.getLogger(__name__)
  39. def configure_logging(verbose: bool = False) -> None:
  40. """Configure console logging."""
  41. logging.basicConfig(
  42. level=logging.DEBUG if verbose else logging.INFO,
  43. format="%(levelname)s: %(message)s",
  44. )
  47. def parse_args(argv: Optional[Sequence[str]] = None) -> argparse.Namespace:
  48. """Parse command-line arguments."""
  49. parser = argparse.ArgumentParser(
  50. description="Export raw image slices and mask slices from a syGlass project."
  51. )
  52. parser.add_argument(
  53. "project_dir",
  54. type=Path,
  55. help="Folder containing the <project_name>.syg project directory.",
  56. )
  57. parser.add_argument(
  58. "project_name",
  59. help="Project name without the .syg suffix, for example: my_project.",
  60. )
  61. parser.add_argument(
  62. "--raw-output-dir",
  63. type=Path,
  64. default=None,
  65. help="Output folder for raw image slices. Default: <project_dir>/raw_images.",
  66. )
  67. parser.add_argument(
  68. "--mask-output-dir",
  69. type=Path,
  70. default=None,
  71. help="Output folder for mask slices. Default: <project_dir>/masks.",
  72. )
  73. parser.add_argument(
  74. "--z-chunk-size",
  75. type=int,
  76. default=16,
  77. help="Number of Z slices to load per chunk. Default: 16.",
  78. )
  79. parser.add_argument(
  80. "--resolution-level",
  81. type=int,
  82. default=-1,
  83. help=(
  84. "syGlass resolution level to export. Default: -1, which is the "
  85. "last available resolution level."
  86. ),
  87. )
  88. parser.add_argument(
  89. "--verbose",
  90. action="store_true",
  91. help="Print additional diagnostic information.",
  92. )
  93. return parser.parse_args(argv)
  96. def resolve_output_dir(
  97. output_dir: Optional[Path], project_dir: Path, default_name: str
  98. ) -> Path:
  99. """Return an output directory path and create it if needed."""
  100. resolved = output_dir if output_dir is not None else project_dir / default_name
  101. resolved = resolved.expanduser().resolve()
  102. resolved.mkdir(parents=True, exist_ok=True)
  103. return resolved
  106. def get_project_resolution(project: object, resolution_level: int) -> Tuple[int, np.ndarray]:
  107. """Return the resolved resolution level and volume shape as ``(Z, Y, X)``."""
  108. resolution_map = project.get_resolution_map()
  109. resolution_count = len(resolution_map)
  111. if not -resolution_count <= resolution_level < resolution_count:
  112. raise ValueError(
  113. f"Invalid resolution level {resolution_level}. Project has "
  114. f"{resolution_count} levels."
  115. )
  117. level_index = resolution_level % resolution_count
  119. block_size = project.get_block_size()
  120. block_count = resolution_map[level_index]
  121. blocks_per_dimension = round(block_count ** (1.0 / 3.0))
  122. resolution = (block_size * blocks_per_dimension).astype(np.uint64)
  124. return level_index, resolution
  127. def export_syglass_project(
  128. project_dir: Path,
  129. project_name: str,
  130. raw_output_dir: Path,
  131. mask_output_dir: Path,
  132. z_chunk_size: int = 16,
  133. resolution_level: int = -1,
  134. ) -> None:
  135. """Export raw-image and mask slices from a syGlass project."""
  136. if z_chunk_size <= 0:
  137. raise ValueError("--z-chunk-size must be a positive integer.")
  139. project_path = project_dir / f"{project_name}.syg"
  140. if not project_path.exists():
  141. raise FileNotFoundError(f"Project directory not found: {project_path}")
  143. LOGGER.info("Opening syGlass project: %s", project_path)
  144. project = sy.get_project(str(project_path))
  145. syglass_project_name = project.get_name()
  147. timepoint_count = project.get_timepoint_count()
  148. if timepoint_count > 1:
  149. LOGGER.warning(
  150. "Timeseries projects are not fully supported by this tool. "
  151. "Only timepoint 0 will be exported."
  152. )
  154. level_index, resolution = get_project_resolution(project, resolution_level)
  155. z_size, y_size, x_size = [int(value) for value in resolution]
  157. LOGGER.info("Loaded project: %s", syglass_project_name)
  158. LOGGER.info("Resolution level: %d", level_index)
  159. LOGGER.info("Export volume shape: Z=%d, Y=%d, X=%d", z_size, y_size, x_size)
  160. LOGGER.info("Raw output folder: %s", raw_output_dir)
  161. LOGGER.info("Mask output folder: %s", mask_output_dir)
  163. mask_extractor = pyglass.MaskOctreeRasterExtractor(None)
  165. for z0 in tqdm(range(0, z_size, z_chunk_size), desc="Exporting Z chunks"):
  166. z1 = min(z0 + z_chunk_size, z_size)
  167. current_chunk_size = z1 - z0
  169. raw_block = project.get_custom_block(
  170. 0,
  171. level_index,
  172. np.asarray([z0, 0, 0]),
  173. [current_chunk_size, y_size, x_size],
  174. ).data
  176. if raw_block.ndim != 4:
  177. raise ValueError(
  178. f"Expected raw block with shape (Z, Y, X, C), got {raw_block.shape}."
  179. )
  181. z_chunk, _, _, channel_count = raw_block.shape
  183. mask_block = mask_extractor.GetCustomBlock(
  184. project.impl,
  185. 0,
  186. level_index,
  187. pyglass.vec3(0, 0, float(z0)),
  188. pyglass.vec3(float(x_size), float(y_size), float(z_chunk)),
  189. )
  190. mask_np = pyglass.GetRasterAsNumpyArray(mask_block)
  192. if mask_np.ndim != 4:
  193. raise ValueError(
  194. f"Expected mask block with shape (Z, Y, X, 1), got {mask_np.shape}."
  195. )
  197. for local_z, global_z in enumerate(range(z0, z1)):
  198. for channel_index in range(channel_count):
  199. raw_filename = (
  200. f"{syglass_project_name}_Image_{global_z:05d}_ch{channel_index}.tiff"
  201. )
  202. tifffile.imwrite(
  203. raw_output_dir / raw_filename,
  204. raw_block[local_z, :, :, channel_index],
  205. )
  207. mask_filename = f"{syglass_project_name}_Mask_{global_z:05d}.tiff"
  208. tifffile.imwrite(
  209. mask_output_dir / mask_filename,
  210. mask_np[local_z, :, :, 0],
  211. )
  213. LOGGER.info("Export complete.")
  216. def main(argv: Optional[Sequence[str]] = None) -> None:
  217. """Command-line entry point."""
  218. args = parse_args(argv)
  219. configure_logging(args.verbose)
  221. project_dir = args.project_dir.expanduser().resolve()
  222. raw_output_dir = resolve_output_dir(args.raw_output_dir, project_dir, "raw_images")
  223. mask_output_dir = resolve_output_dir(args.mask_output_dir, project_dir, "masks")
  225. export_syglass_project(
  226. project_dir=project_dir,
  227. project_name=args.project_name,
  228. raw_output_dir=raw_output_dir,
  229. mask_output_dir=mask_output_dir,
  230. z_chunk_size=args.z_chunk_size,
  231. resolution_level=args.resolution_level,
  232. )
  235. if __name__ == "__main__":
  236. main()

export_syglass_volume.py at commit 90a5232, under CC-BY-NC-4.0 · at the source

Overview

Authors: Kayleigh S Scotcher1, John‐Paul Fuller‐Jackson1, Peregrine B Osborne1, Martin M Bertrand2, Janet R Keast1
ORCID iDs: Kayleigh S Scotcher, Peregrine B Osborne
  1. Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
  2. IMAGINE UR‐UM 103, Faculté de Médecine Montpellier‐Nîmes, Montpellier, France
Institutions: The University of Melbourne (Australia); Initial MAnagement and prevention of acute orGan failures IN critically ill patiEnts
Journal: Journal of anatomy, article 10.1111/joa.70213
Dates: received 12 January 2026; accepted 1 July 2026; published online 23 July 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1111/joa.70213 · PMID 42494090 · PMCID PMC13396685 · OpenAlex W7170572325
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: histology / microscopy (modality), human (organism)
Methods: Machine learning
Keywords: light sheet microscopy, neuroanatomy, pelvic visceral organs, sympathetic ganglia, sympathetic nervous system, tissue clearing
Topic: Gastrointestinal motility and disorders (Gastroenterology, Medicine), according to OpenAlex
Citations: cited by 1 paper (Europe PMC); 90 references in the paper

Abstract

The superior hypogastric plexus (SHP) and hypogastric nerves (HN) are components of the autonomic nervous system required for sympathetic regulation of the pelvic viscera. Despite their functional importance, the three‐dimensional (3D) distribution and immunohistochemical composition of neurons in these structures remain poorly characterized. In this study, we used a multiscale imaging approach to generate a 3D anatomical and immunohistochemical characterization of the SHP and HN in adult humans. Both embalmed (body donor program) and unembalmed paraformaldehyde (PFA)‐fixed specimens (organ donor program) were cleared using a modified Adipo‐Clear/iDISCO protocol and imaged by light sheet fluorescence microscopy. Thousands of neuronal cell bodies were identified within the HN, demonstrating that this nerve does not function solely as a conduit for axons. In one HN sample analyzed along its whole length by immunohistochemistry, more than 90% of the neurons were tyrosine hydroxylase‐immunoreactive (TH‐IR), so presumed to be noradrenergic. Neuronal cell bodies in both the SHP and HN were arranged in clusters of diverse size, embedded within nerve tracts rather than in discrete ganglia. High‐resolution confocal microscopy of cryosections confirmed the presence of numerous TH‐IR (presumed noradrenergic) neuronal cell bodies and axons in the SHP and HN. Non‐noradrenergic axonal populations were also abundant. Putative afferent axons (calcitonin gene‐related peptide‐ and substance P‐immunoreactive) traversed the SHP and HN and occasionally encircled individual ganglion neurons, raising the possibility of direct sensory‐motor communication at these sites. Collectively, these findings provide a new 3D anatomical and immunohistochemical characterization of the SHP and HN in the adult human. This has important implications for understanding normal pelvic autonomic function and pathophysiology of genitourinary disorders. These data and further application of our imaging approach will inform the improvement of nerve‐sparing surgical techniques in the pelvic region and the development of targeted neuromodulation approaches.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

alicia-ziying-yang/syglass-multichannel-io-utils

License: CC-BY-NC-4.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 90a5232119aee28f1ae21aac1e67fcba3a8b3c69, 16 July 2026
Languages: Python (2)
Size: 6 files, 2 scripts
Software Heritage: not archived
Found in: the text, “Cleared tissue: Light sheet fluorescence microsc”
Holds: README, license file, CITATION.cff, environment (requirements.txt)
Not found: tests, continuous integration, documentation
Tools: NumPy (2 files), tifffile (2 files)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
4 files
At the source: github.com/alicia-ziying-yang/syglass-multichannel-io-utils

Tracing map

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  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 2 scripts, each with its path and the digest of its content;
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No dataset and no data link were found in the paper.

Data availability statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, pages, dates, 5 authors, 6 keywords, 90 references.

Cite

This paper

Scotcher, K. S., Fuller‐Jackson, J., Osborne, P. B., Bertrand, M. M., & Keast, J. R. (2026). Multiscale analysis of the adult human superior hypogastric plexus and hypogastric nerve. Journal of anatomy, 10.1111/joa.70213. https://doi.org/10.1111/joa.70213

BibTeX

@article{scotcher2026multiscale,
author = {Scotcher, Kayleigh S and Fuller‐Jackson, John‐Paul and Osborne, Peregrine B and Bertrand, Martin M and Keast, Janet R},
title = {{Multiscale analysis of the adult human superior hypogastric plexus and hypogastric nerve}},
journal = {Journal of anatomy},
year = {2026},
month = jul,
pages = {10.1111/joa.70213},
publisher = {Wiley},
issn = {0021-8782},
doi = {10.1111/joa.70213},
url = {https://doi.org/10.1111/joa.70213},
pmid = {42494090},
pmcid = {PMC13396685}
}

RIS

TY - JOUR
AU - Scotcher, Kayleigh S
AU - Fuller‐Jackson, John‐Paul
AU - Osborne, Peregrine B
AU - Bertrand, Martin M
AU - Keast, Janet R
TI - Multiscale analysis of the adult human superior hypogastric plexus and hypogastric nerve
T2 - Journal of anatomy
J2 - J Anat
PY - 2026
DA - 2026/07/23
SP - 10.1111/joa.70213
SN - 0021-8782
PB - Wiley
DO - 10.1111/joa.70213
UR - https://doi.org/10.1111/joa.70213
LA - en
ER -

CSL-JSON

{
"id": "10.1111/joa.70213",
"type": "article-journal",
"title": "Multiscale analysis of the adult human superior hypogastric plexus and hypogastric nerve",
"container-title": "Journal of anatomy",
"author": [
{
"family": "Scotcher",
"given": "Kayleigh S"
},
{
"family": "Fuller‐Jackson",
"given": "John‐Paul"
},
{
"family": "Osborne",
"given": "Peregrine B"
},
{
"family": "Bertrand",
"given": "Martin M"
},
{
"family": "Keast",
"given": "Janet R"
}
],
"container-title-short": "J Anat",
"page": "10.1111/joa.70213",
"DOI": "10.1111/joa.70213",
"PMID": "42494090",
"PMCID": "PMC13396685",
"ISSN": "0021-8782",
"publisher": "Wiley",
"URL": "https://doi.org/10.1111/joa.70213",
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
23
]
]
}
}

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