NeuroQP

Capabilities

Atlases

Register mouse brain, rat brain and spinal cord sections, even when they are cut at an angle.

Mouse, rat and spinal cord atlases

Register every section to a standard reference atlas: the Allen Mouse Brain Atlas, the Kim Unified Mouse Brain Atlas for finer subregions, the Waxholm Sprague Dawley atlas for rat brains, or the Allen Mouse Spinal Cord Atlas. More atlases are on the way.
  • Allen Mouse Brain Atlas, coronal section at AP +1.00 mm, regions in atlas colours

    Allen Mouse Brain Atlas

    The standard reference for mouse brain studies.

    mouse brain · 643 regions · 25 µm

    Wang et al. 2020
  • Kim Unified Mouse Brain Atlas, coronal section at AP −2.50 mm, regions in atlas colours

    Kim Unified Mouse Brain Atlas

    Finer subregions, with Allen and Franklin-Paxinos labels unified.

    mouse brain · 1,001 regions · 20 µm

    Chon et al. 2019
  • Allen Mouse Spinal Cord Atlas, transverse section at segment C6, regions in atlas colours

    Allen Mouse Spinal Cord Atlas

    Every segment from cervical to coccygeal.

    mouse spinal cord · 73 regions · 10 µm

    Fiederling et al. 2021
  • Waxholm Sprague Dawley Rat Brain Atlas, coronal section at AP −2.00 mm, regions in atlas colours

    Waxholm Sprague Dawley Rat Brain Atlas

    An open reference for the adult rat brain.

    rat brain · 224 regions · 39 µm

    Kleven et al. 2023

★ Our most popular feature

Make the atlas fit your tilted sections

Few cuts are perfectly coronal. At the surface of a mouse brain, a couple of degrees of tilt puts the two hemispheres at different AP positions, so a flat coronal atlas can't match both sides. NeuroQP lets you tilt the atlas to match the section.

  • Adjust left/right and dorsal/ventral tilt, with a live preview in both viewers
  • Set tilt once per animal; every slice keeps its own AP and landmarks
  • Counts, areas, overlays and density plots all use the tilted geometry

Kim mouse atlas · target AP −1.30 mm from Bregma

AP −1.30 mm0.00 mm
Kim mouse atlas section at AP −1.30 mm, tilted 0° left-right and 0° dorsal-ventral
AP −1.30 mm0.00 mm

Left AP −1.30 · Right AP −1.30 mm

Left–right tilt 0°

APML
CoronalSection
Top view

Dorsal–ventral tilt 0°

DV−AP
Side view

Sketch angles exaggerated 2×

Spinal cord, segment by segment

Spinal cord sections get the same workflow as brain sections. Register each section to the Allen Mouse Spinal Cord Atlas, count cells by anatomical region, and compare across cervical, thoracic, lumbar and sacral levels.

  • Name sections by segment (C1, T9, L3) instead of exact coordinates
  • Dorsal horn, ventral horn and white matter as quantifiable regions
  • Same detection, classifiers and statistics as brain projects

Allen mouse spinal cord atlas · 34 segments

C6Cervical · 2.64–3.22 mm
Allen mouse spinal cord atlas, segment C6
Cervical
Thoracic
Lumbar
Sacral
Coccygeal

Left and right, separately or together

Lateralized injections, unilateral lesions and asymmetric effects are easy to quantify. Measure the regions where hemisphere matters separately and keep the rest joint.

  • Separate left/right measurements in tables, viewers and plots
  • Choose joint or separate for each region

Kim mouse atlas · AP −1.70 mm

Selected regions

Joint: both hemispheres togetherSeparate: left and rightTap a region in the list or on the atlas.

Bring your tilted sections, spinal cords and rat brains.

Upload, review, and export region-level results without plugins, scripts, or a GPU.

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