Multimodal Biomedical Dataset for Evaluating Registration Methods (patches from TMA Cores)

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 Aligned Collagen Is a Prognostic Signature for Survival in Human Breast Carcinoma (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.