DOI: 10.5281/zenodo.3874362
title: Multimodal Biomedical Dataset for Evaluating Registration Methods (patches from TMA Cores)

description: The dataset consists of 206 aligned Bright-Field (BF) and Second-Harmonic Generation (SHG) images. All images are of the same size of 834x834 pixels. The training set contains 40 image pairs. A validation set 1 of 25 image pairs for tuning the hyperparameters for the training. A validation set 2 of 7 image pairs for tuning the registration method. The test set for evaluation: 134 image pairs (times two). For each image pair in the test set, a random rotation up to +/-30 degrees and random translations in x and y for up to 100px were applied. For each image pair that was transformed for the test set, we apply the transformation to both modalities and keep their corresponding reference images as well as transformed images, in order to allow for registration using each modality as a reference and the other as a floating image. The metadata.csv file includes the coordinates of the four corners of the reference image as well as the coordinates of the corners of the transformed image after displacement. The origin of this coordinate system is the upper left corner of the reference image, given by (0,0). Example of naming convention in the test set: R_1B_F8_BF.tif: reference image in Bright-Field R_1B_F8_SHG.tif: reference image in Second-Harmonic Generation T_1B_F8_BF.tif: transformed image in Bright-Field T_1B_F8_SHG.tif: transformed image in Second-Harmonic Generation. Where the transformations applied to T_1B_F8_BF.tif and T_1B_F8_SHG.tif are identical and hence the coordinates of the corners in metadata.csv are valid for both image pairs. The metadata.csv file contains the following columns: Filename: identifier for image pair X1_Ref: x-coordinate of upper left corner of reference image Y1_Ref: y-coordinate of upper left corner of reference image X2_Ref: x-coordinate of lower left corner of reference image Y2_Ref: y-coordinate of lower left corner of reference image X3_Ref: x-coordinate of upper right corner of reference image Y3_Ref: y-coordinate of upper right corner of reference image X4_Ref: x-coordinate of lower right corner of reference image Y4_Ref: y-coordinate of lower right corner of reference image X1_Trans: x-coordinate of upper left corner of transformed image Y1_Trans: y-coordinate of upper left corner of transformed image X2_Trans: x-coordinate of lower left corner of transformed image Y2_Trans: y-coordinate of lower left corner of transformed image X3_Trans: x-coordinate of upper right corner of transformed image Y3_Trans: y-coordinate of upper right corner of transformed image X4_Trans: x-coordinate of lower right corner of transformed image Y4_Trans: y-coordinate of lower right corner of transformed image Displacement: Mean Euclidean distance between reference corner points and transformed corner points The data set was originally produced by the authors of <em>Aligned Collagen Is a Prognostic Signature for Survival in Human Breast Carcinoma</em> (https://www.sciencedirect.com/science/article/pii/S0002944010002336). The registered and non-registered sub-image pairs in this data set were created by Johan Öfverstedt and Elisabeth Wetzer.