This is the first challenge of NeuroCluedo for comparison of neuron detection methods. Launch: april 6th 2021 Organized by: NeuroCluedo **Basic Information** A set of 107 RBG images of full transversal sections form mice spinal cord. The set is divided in: - Comparison subset: 20 images. For comparing detection methods. Do not use for training or validating detection algorithms. - Training subset: 87 images. 3 types of detection methods and participation are considered: - Manual: participants are provided with 12 images from the comparison set to be counted following a defined procedure (requires FIJI ot ImageJ). - Untrained semiautomatic or automatic methods: participants get access to the full comparison set for analysis. - Trained methods (IA): participants get access to the training and validation subset to train the algorithms and validate them. Once the algorithm is completed, the organizer will use it to analyse the comparison set. To participate, please get in contact with us at mnietod@sescam.jccm.es **Additional information** Source of images: Reigada *et al*., 2015. (https://www.sciencedirect.com/science/article/abs/pii/S0306452215004789) Raw images: the original confocal images are available at the repository (https://osf.io/qe9ys/) Species: *Mus musculus* strain C57BL/6J Conditions: includes naive and injured spinal cord sections distributes - Sham (2 individuals, N images). Laminectomy without injury - Vehicle - UCF-101 Histology: perfusion with saline and PFA 4%, fixation in PFA 4%, ... 20µm thick sections. Staining: - DAPI - NeuN-Alexa 594 Microscopy: confocal ... Image processing (imageJ): - Maximum Intensity Projection - Conversion to RBG tiff format **Files** - tif images folder: folder comprising 2 zip files that contain the tif images of the comparison (20 images) and training sets (87 images) - Threshold ID_macro.txt: ImageJ / fiji macro for neuron thresholding developed and employed for Reigada et al. (2015) study (in txt format) - Threshold ID_idetifications.zip: zip file containing 20 tif files with the neuronal identifications derived obtained with the threshold macro. - Manual ID_Spreadsheet for data collection.xlsx: Excel spreadsheet employed by the observers for data collection. Includes instructions. (xlsx file) - Manual ID_identifications xml.zip: Folder containing the neuronal identifications of each observer in eahc image. Data is presented in xml format exported from the count tool of imageJ or fiji. - Neuronal Network_NC_AI1.nn: Neuronal network developed in this study. In .nn format of Cell Sense Diensions (Olympus) software. To be used with Cel Sense Dimensions software. - Neuronal Network_ground truth.zip: Zip compressed folder comprising the different types of files employed to train the Neuronal network. - Neuronal Network_Identifications.zip: Zip compressed folder containing the tif files of the comparisin set with the Neuronal network identifications. Neuronal Network_ImageJ macro.ijm Macro to identify as neurons those particles above 25 µm2 composed of pixels above 50% probability according to the neuronal networki. - Ibañez 2021_Degree Project_in spanish.pdf: Final degree project of Nadia Ibañez Barranzo describing most results of this test bench (pdf, in spanish)