Julian Cooper
Hirsch Lab

An RGB deep-neural network approach for high-throughput phenotyping of Fusarium head blight in wheat

File contents:

1_fhb_disease_data: Fusarium head blight field and image data frames and analysis
- FHB_disease_human_field: For each row/plot at each rating date/location, 0-100% plot average disease scores from five raters, A-E.
- FHB_disease_pipeline_image: For each row/plot at each rating date/location, individual spike disease percentage (fhb_percentage) and gradability classification (gradability_prob, <0.50  = gradable) for all detected wheat heads.
- FHB_disease_human_pipeline_200image: For the 200 spike images used to measure inter-rater reliability, individual spike disease percentage from each rater, A-E, and from the FHB image analysis pipeline (Pipeline).
- FHB_disease_human_pipeline_10Kimage: For all spikes determined to be gradable by raters during manual image annotation of the 10K images used to compare human and pipeline disease annotations on a spike and plot level, individual spike disease percentage from the FHB image analysis pipeline (pipeline_image_perc_FHB) and from manual image annotation by a human rater (human_image_perc_FHB) as well as the rater ID. 

2_image_analysis_pipeline_workflow: Image analysis pipeline for analyzing images 
3_wheat_spike_detection_model: Contains grain_head_and_other_detection model for wheat spike detection to be loaded into image analysis pipeline
4_wheat_spike_gradability_model: Contains umn_full_growth_cycle_unet_128x128 model for wheat spike gradability classification to be loaded into image analysis pipeline
5_wheat_spike_segmentation_model: Contains wheat_head_fhb_seg model for wheat spike segmentation to be loaded into image analysis pipeline
6_disease_segmentation_model: Contains wheat_spike_fhb_disease_non_gradable_classification_input_is_BGR model for disease segmentation to be loaded into image analysis pipeline

7_n200_inter_rater_reliability_images: Five raters and pipeline annotating disease on same 200 spikes to compare inter-rater reliability
- Pipeline: Raw images and disease annotations from the FHB image analysis pipeline
- raterA: Raw images and manual images annotations of FHB disease by rater A
- raterB: Raw images and manual images annotations of FHB disease by rater B
- raterC: Raw images and manual images annotations of FHB disease by rater C
- raterD: Raw images and manual images annotations of FHB disease by rater D
- raterE: Raw images and manual images annotations of FHB disease by rater E

8_rover_20220713_StP_images_1-4: Raw rover images of Fusarium head blight on wheat from camera C and D for Saint Paul, MN on July 13th 2022 used for FHB image analysis pipeline evaluation
9_rover_20220718_StP_images_1-4: Raw rover images of Fusarium head blight on wheat from camera C and D for Saint Paul, MN on July 18th 2022 used for FHB image analysis pipeline evaluation
10_rover_20220720_StP_images_1-4: Raw rover images of Fusarium head blight on wheat from camera C and D for Saint Paul, MN on July 20th 2022 used for FHB image analysis pipeline evaluation
11_rover_20220728_Crk_images_1-4: Raw rover images of Fusarium head blight on wheat from camera C and D for Crookston, MN on July 28th 2022 used for FHB image analysis pipeline evaluation