Dorsal horn mapping: a Fiji toolbox for standardized laminar registration and transparent reporting of spinal cord imaging data from adult C57Bl/6 mice.
- 1Department of Anesthesiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
Abstract
Introduction
Rexed's laminae provide the anatomical framework for interpreting the spatial organization of neuronal populations within the spinal dorsal horn and are therefore widely used to describe immunohistochemical, in situ hybridization, and functional imaging data. However, despite their widespread use, no standardized approach for assigning cells to individual laminae has been established, limiting reproducibility and direct comparison of datasets across studies.Methods
We developed Dorsal Horn Mapping, an open-source Fiji toolbox that implements a standardized workflow for laminar registration in transverse mouse spinal cord sections. The toolbox aligns segment-specific reference maps to experimental images using user-guided rigid transformations and independent scaling, assigns labeled cells to Rexed's laminae, and transforms their positions into a common spatial reference frame. In addition, it provides tools for quantitative laminar analysis and visualization of pooled datasets as composite reference maps.Results
Validation experiments demonstrated high inter-user reproducibility of template alignment and laminar assignment across users with different levels of anatomical expertise. Registrations showed good agreement with established laminar markers and resulted in highly consistent assignment of neuronal populations to individual laminae. Thus, 81% of IB4-pos pixels were mapped to lamina II (95% CI: 68.4-86.2%) and the estimated difference in cell counts averaged across all users, segments and laminae was 0.08 cells (95% CI: -0.68 to 0.83; P = 0.843). Analysis of representative multichannel immunohistochemical datasets further demonstrated the utility of the workflow for standardized visualization and quantitative analysis of cellular localization.Conclusion
Dorsal Horn Mapping provides an accessible framework for standardized laminar registration and transparent spatial reporting of spinal cord imaging data from adult C57BL/6 mice. By introducing a common spatial reference system for dorsal horn anatomy, the toolbox facilitates direct comparison of cellular localization across experiments and laboratories and has the potential to improve reproducibility, comparability, and reporting standards in pain and spinal cord research.
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BibTeX
@article{roettger2026dorsal,
title = {{Dorsal horn mapping: a Fiji toolbox for standardized laminar registration and transparent reporting of spinal cord imaging data from adult C57Bl/6 mice.}},
author = {L Roettger and P Adamek and S G Lechner},
journal = {Frontiers in pain research (Lausanne, Switzerland)},
year = {2026},
month = oct,
doi = {10.3389/fpain.2026.1961590},
url = {https://europepmc.org/article/MED/42908979},
note = {CC BY},
}
RIS
TY - JOUR
TI - Dorsal horn mapping: a Fiji toolbox for standardized laminar registration and transparent reporting of spinal cord imaging data from adult C57Bl/6 mice.
AU - L Roettger
AU - P Adamek
AU - S G Lechner
PY - 2026
DA - 2026/10/07
JO - Frontiers in pain research (Lausanne, Switzerland)
DO - 10.3389/fpain.2026.1961590
UR - https://europepmc.org/article/MED/42908979
AB - Introduction Rexed's laminae provide the anatomical framework for interpreting the spatial organization of neuronal populations within the spinal dorsal horn and are therefore widely used to describe immunohistochemical, in situ hybridization, and functional imaging data. However, despite their widespread use, no standardized approach for assigning cells to individual laminae has been established, limiting reproducibility and direct comparison of datasets across studies.Methods We developed Dorsal Horn Mapping, an open-source Fiji toolbox that implements a standardized workflow for laminar registration in transverse mouse spinal cord sections. The toolbox aligns segment-specific reference maps to experimental images using user-guided rigid transformations and independent scaling, assigns labeled cells to Rexed's laminae, and transforms their positions into a common spatial reference frame. In addition, it provides tools for quantitative laminar analysis and visualization of pooled datasets as composite reference maps.Results Validation experiments demonstrated high inter-user reproducibility of template alignment and laminar assignment across users with different levels of anatomical expertise. Registrations showed good agreement with established laminar markers and resulted in highly consistent assignment of neuronal populations to individual laminae. Thus, 81% of IB4-pos pixels were mapped to lamina II (95% CI: 68.4-86.2%) and the estimated difference in cell counts averaged across all users, segments and laminae was 0.08 cells (95% CI: -0.68 to 0.83; P = 0.843). Analysis of representative multichannel immunohistochemical datasets further demonstrated the utility of the workflow for standardized visualization and quantitative analysis of cellular localization.Conclusion Dorsal Horn Mapping provides an accessible framework for standardized laminar registration and transparent spatial reporting of spinal cord imaging data from adult C57BL/6 mice. By introducing a common spatial reference system for dorsal horn anatomy, the toolbox facilitates direct comparison of cellular localization across experiments and laboratories and has the potential to improve reproducibility, comparability, and reporting standards in pain and spinal cord research.
SN - 2673-561X
ER -