Docker container details

The challenge organizers will provide a bash script `register` that is intended to register all the image pairs in the test set. The participants are asked to modify this file to call their dockerized registration implementations. You can download `register` script here: register

The container can either contain all the executed code or only the environment.  In the latter case, the algorithm can be provided e.g. in a zip file along with the container.

The container entrypoint can be specified to allow execution in the following manner:

docker run container-name register /path/to/input_table.csv

The `register` script is given the following arguments:

• path_table_csv - a list of files and landmarks to register
• path_images_dir - path to the images directory
• path_annot_dir - path to the landmarks directory
• path_output_dir - path to output directories

path_table_csv will contain filenames needed for registration.
It has the following columns:

• wsi_source - moving image name
• wsi_target - fixed image name
• landmarks_csv - landmarks file name
• output_dir_name - name of the output directory

landmarks_csv has the following format:

• x_source - x coordinate
• y_source - y coordinate
• mpp_source - moving image resolution in μm / pixel
• mpp_target - fixed image resolution in μm / pixel

Output directory 'output_dir_name' should contain these files after registering a pair of images:

• registered_source_image.tiff (or any other lossless format, compressed (e.g. LZW), 1.25x magnification i.e. 10x/8)
• registered_landmarks.csv (has columns x_target and y_target)

1.25x magnification equals downscaling each dimension of the highest available 10x resolution by a factor of 8. Please use lossless compression to save the file (LZW for example). Point coordinates in both landmark files are given in micrometers and should contain the same number of points.

To help with creating the container for your final submission, here you can download files for the validation set compatible with the final submission format: Container test files

Submission

Once you are ready to submit your container for evaluation, please send an email to masi.f.valkonen@utu.fi to receive an upload voucher. Only the last submission through the upload service is taken into account.