Rules

• Participants agree to submit a .zip file that includes dense deformation fields for each of the volume pairs within the test set, and a brief write-up explaining their approaches. The write-up should include an algorithm speed assessment, which includes the runtime of each algorithm as well as information about the host environment (machine type, the number of cores or GPUs used, and the amount of Ghz that each processing unit supports). The template for the write-up will be provided by the committee. 

• Participants agree to register with their real names, affiliation, and affiliation email. 

• Participants agree to cite any additional datasets or pre-trained models used during the competition. 

• Solutions should be automatic; participants agree to not create hand-annotations for the data. 

• Participants should not join more than one team. 

Submission Format

Files

For each species, please upload a .zip file to the species-specific leaderboard. The .zip file for the test dataset should contain a parent directory named submission with one of three files inside: zebrafish_test.h5, mouse_test.h5 or c_elegan_test.h5. Each of the .h5 files should contain HDF5 datasets named pair[x], where x is the pair number being aligned . The content of each HDF5 dataset should be the dense deformation field for that respective pair, saved as an array.  Below is a visual overview of the file structure.

For the zebrafish leaderboard: 

parent directory: submission

     |_ zebrafish_test.h5 

          |_ HDF5 dataset: pair5 (please save with gzip compression)

          |_ HDF5 dataset: pair6 (please save with gzip compression)

          |_ HDF5 dataset: pair7 (please save with gzip compression)

For the mouse leaderboard: 

parent directory: submission

     |_ mouse_test.h5 

          |_ HDF5 dataset: pair5 (please save with gzip compression)

          |_ HDF5 dataset: pair6 (please save with gzip compression)

          |_ HDF5 dataset: pair7 (please save with gzip compression)

For the C. elegans leaderboard: 

     |_ c_elegan_test.h5 

          |_ HDF5 dataset: pair5 (please save with gzip compression)

          |_ HDF5 dataset: pair6 (please save with gzip compression)

          |_ HDF5 dataset: pair7 (please save with gzip compression)

We also ask that participants upload metadata under the "supplemental file" section. The metadata should provide the runtime, host environment, and a brief description of the model used to generate each deformation field. The template for the metadata file (.json) can be found here. Please note that Grand Challenge does not accept .json files directly. Before submission, participants will need to copy and paste the contents of their created .json into a .txt file. Participants will have the opportunity to submit to each leaderboard four times per day. 

Deformation Field

Given a pair of 3D image volumes to register (fixed volume and moving volume), the submitted deformation field should be represented by a 4D numpy array of shape (D, H, W, 3), where D, H, and W are the depth (or the number of Z-slices), height, and width of the fixed volume. The 3-vector (z, y, x) at each voxel index (k, j, i) represents a displacement vector pointing to the corresponding voxel coordinates in the moving volume. In other words, it indicates the voxel at (k, j, i) in the fixed volume corresponds to the voxel at (k+z, j+y, i+x) in the moving volume. Please note that the axis order is ZYX, not XYZ. Also note that the coordinates are in voxels, equivalent to assuming that the voxel size is (1, 1, 1). Please make sure to use voxel coordinates for submission, especially if the physical voxel size is used in the registration algorithm, as displacement vectors may need to be rescaled. Deformation maps should be cast into 32-bit arrays and rounded to the second decimal place. Please see our script for an example on how to do this.