Original images, ground truth annotations, and precited masks from U-NET for a fungal species x nitrogen experiment

This document describes the “MicroVision-MV003” dataset.

This folder contains three subfolders: “originals”, “predicted_masks”, and “gt_masks”.

The “originals” folder contains 720 original images acquired using two imaging modalities: 360 images from overhead imaging and 360 images from transmission (raw) imaging.

Naming scheme:
YYYY-MM-dd__plate_strain_nitrogen-level_replication_experiment_imaging-modality
YYYY-MM-dd: 2024-12-20, 2024-12-21, 2024-12-22,2024-12-23,2024-12-24,2024-12-25,2024-12-26,2024-12-27,2024-12-28,2024-12-29,2024-12-30,2024-12-31.
plate: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30.
strain: FG, LE.
nitrogen-level: N-1, N-10, N-100.
replication: 1, 2, 3, 4, 5.
experiment: MV.003.
imaging-modality: overhead, transmission (raw).

For example, the image
2024-12-20__1_FG_N-10_3_MV.003_overhead
was taken on 2024-12-20. The plate number is 1, the fungal strain is FG, the nitrogen treatment is N-10, and the replication number is 3 for experiment MV.003, acquired using the overhead imaging modality. FG is Fusarium grammanirum. LE is Linnemannia elongata.

The “predicted_masks” folder contains masks generated by a trained U-Net model for the transmission imaging modality.
The “gt_masks” folder contains 326 human hand-traced masks that serve as ground truth.

This data was produced by Plant Microbe Interfaces SFA at ORNL. This research was sponsored by the U.S. Department of Energy, Office of Science, Biological and Environmental Research, Genomic Science Program as part of the Plant-Microbe Interfaces Science Focus Area (http://pmi.ornl.gov; under FWP ERKP730). Oak Ridge National Laboratory is managed by UT-Battelle LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.