Training, validation, and test images of intact (Uninjured/Sham) and moderately contused thoracic spinal cord cross-sections of adult female C57BL/6J mice. Tissue sections are immunostained for NeuN (Rbfox3) and DAPI. This dataset is released in SpineDL paper and it is composed by two parts: Structure identification: semantic segmentation of spinal cord regions. Classes: Background (0), White matter (1), Ependyma (2), Gray matter (3), Lesioned / damaged tissue (4). Neuron identification: instance-level identification of neuronal somas. Each instance has a unique integer value. For more detailed information regarding the images, sectioning protocols, and individual animal data, please refer to the attached Excel file: “Image information.xlsx”. The original raw confocal images, along with more extensive documentation, are available on the Open Science Framework (OSF). Data type: Paired fluorescence microscopy and segmented mask images for spine structures and neurons Microscopy data type: 2D widefield images (fluorescence) and masks obtained via manual segmentation (see https://osf.io/n32z9 for details on segmentation). Microscope: Leica high-speed confocal systems (High-Speed Confocal Scanner and Leica TCS SP5) with 20X objective. Tissue type: female mouse thoracic spinal cord from injured and uninjured female C57BL6/ mice File format: .tif (8 and 16 bits) and .xml for neuronal labels in test images Image size: full spinal cord sections of variable size (up to 5000x5000 pixels). Pixel size: 1.12 to 2.25 µm Image preprocessing: Original z-stack confocal images were acquired with the LAS-AF 2.3 system and processed in Fiji. Processing included removing non-DAPI/NeuN channels, generating a maximal projection, assigning NeuN to red, and standardizing channel order Funding bodies: Council of Education, Culture and Sports of the Regional Government of Castilla-La Mancha (Spain), co-funded by the European Union (FEDER) Author(s): Pablo Ruiz-Amezcua (1,5), Daniel Franco-Barranco (2,3,4), David Reigada (1), Teresa Muñoz-Galdeano (1), Rodrigo Martinez Maza (1), Manuel Nieto-Díaz (1) Contact email: daniel.franco@dipc.org Affiliation: 1) Hospital Nacional de Parapléjicos (SESCAM). Toledo, Spain2) MRC Laboratory of Molecular Biology, Cambridge, UK3) Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK4) Donostia International Physics Center (DIPC), San Sebastián, Spain5) Department of Experimental Biology, University of Jaén, Jaén, Spain Associated publications: In progress