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Drone Data Processing

Upload Data

To navigate to the file upload page, click on the Upload Icon.

Data Types

Image Data: This is the raw image files taken from the sensing platforms. These group of images should be coming from an individual sensor. Some image types include: jpg, jpeg, png or tif

GCP Locations: This is a csv file containing locations of GCPs. The first column should contain the label, the second column contains latitude and the third column contains longitude.

Example GCP Locations

GCP Locations

Data Fields

Year: This is the year YYYY the data was collected. It is a required field. For example, 2022 is a valid year.

Experiment: This is open for the user to decide. This will differentiate experiments for a single year. For example, Experiment 1 is a valid experiment.

Location: This is the location where the data was collected. For example, Davis is a valid location.

Population: This is the type of plants you will be analyzing. For example, Legumes is a valid population.

Date: This is the date YYYY-MM-DD the data was collected. It is a required field. For example, 2022-06-20 is a valid date.

Platform: This is the sensing platform used to collect the data. For example, Drone is a valid platform.

Sensor: This is the data type collected. For example, RGB or Thermal are valid sensors.

Upload Files

  1. Choose the Data Type you want to upload.
  2. Fill in the respective fields.
  3. Drag and drop your files in the upload region.
    Upload File

Video Demonstration

File Upload Video

Manage Files

Data Table

  • Navigate to the Manage Files tab to view uploaded data and prepare for processing.
  • Hover over any of the action buttons in the Actions column to see their function.

Orthomosaic Generation

To navigate to the image processing page, click on the Process Icon. Use the icon with three lines to open and close the data selection menu.

OpenDroneMap

  • NOTE: To maximize orthomosaic output resolution, upload a gcp_locations.csv file in the Upload tab.
  • You can also upload the GCP file right after selecting Start in the dropdown.
  • Under the Orthomosaic Method dropdown, select OpenDroneMap. This is recommended for Aerial data with vertical and horizontal overlap.
  • After uploading image files to the app, orthomosaic generation can be performed.
  • Expand the dropdown menu of the correct platform and sensor type to select the date to perform generation on.
  • Click the Start button to open the orthomosaic generation window. Use the Previous and Next buttons or the selection bar to iterate through images to mark all visible ground control points (GCPs) if a GCP Locations file was uploaded. If a GCP is placed in error, points can be removed by right-clicking.
  • When ready to proceed, click Generate Orthophoto. In the settings dropdown, select the orthophoto quality. The Custom option can be used with OpenDroneMap args if more specific settings are needed. The default setting attempts to use a GSD (Ground Sampling Distance) of 0.01 cm/pixel. Use the Custom option to input specific GSD values if desired.
  • After selecting the quality level, click Process Images.
  • Follow the progress of orthomosaic generation by observing the progress bar at the bottom of the page. Progress can also be monitored via the logs, which can be opened using the arrow on the right side of the progress bar.
  • Processing may take up to 2 hours with large image datasets. To decrease processing time, use the Custom setting with an increased orthophoto-resolution flag. For example, the Custom setting with --orthophoto-resolution 1.0 would decrease processing time by a large amount.
  • If any issues are seen with the output orthophoto using the viewer in the Manage Orthomosaics window, check the GEMINI-App-Data/temp/project/code/odm_report/report.pdf file for more details on the issues / GCP errors encountered during processing.

Plot Boundary Preparation

Import Data

  • After ortho generation is finished, the plot boundary is prepared before further processing.
  • First, input a field_design.csv file in the requested format:

Import Data

Example Field Design

Field Design

  • After uploading, verify that the preview of your data looks correct. If your file has column headers, leave the Data has headers box checked. Click Choose columns.

Preview Data

  • Drag and drop the columns into the appropriate headers used by the app. Navigate through the columns using the left / right arrows. Click Import once all required fields are filled. If columns have titles that exactly match those used by the app, the app's field will be filled automatically.

Select Columns

Population Boundary

  • After importing data, select the date of the data processing will be done on from the dropdown. Navigate to the location of the orthomosaic in the map.
  • Choose the Draw option on the right of the screen. Click along the outer perimeter of the portion of the orthomosaic you'd like to process. Use the Edit, Translate, and Select options to modify the boundary as needed. When finished, click Save.
  • Click Proceed to continue to the Plot Boundary.

Population Boundary

Plot Boundary

  • NOTE: ALL PLOTS with plot boundaries created must be included in Field Design file even if the plots aren’t being used in the field. Without their inclusion, mapping of accession information will be incorrect.
  • Select the orthomosaic once more from the dropdown menu. Click the icon at the bottom left to populate parameters for the plot boundaries.
  • Adjust the parameters until you are satisfied with the plot boundaries for trait extraction.
  • Use the options in the top right to modify the placement of individual rectangles, or all at once using Select All.
  • When finished, click Save. Plot Boundary

Trait Extraction

  • After preparing the plot boundary, aerial traits can be processed.
  • To process traits, click Start on the appropriate date's traits column. Click Analyze to begin processing.
  • If traits need to be processed more than once, click on the blue checkbox and click Analyze again.
  • In the future, the Teach Traits tab will allow for use of trainable aerial models.

Trait Viewing

To navigate to the statistics page, click on the Stats Icon. Use the icon with three lines to open and close the data selection menu.

Statistics Page

  • The stats page shows processed data in tabular and graphical formats.
  • To see statistics from a given date, expand the dropdown menu of the proper platform and sensor type.

  • Click Load on the date's table or graph column to view the extracted trait data.

  • For the tabular format, you will see a window showing the table of traits. If desired, Download CSV can be clicked for the table as a CSV file.

Tabular Statistics

  • For the graphical format, you will see a window showing a bar graph representing the number of plots that fell within certain ranges for the currently selected trait.
  • To view the graph of a different trait, change the selected trait at the top of the window.
  • To view the distribution of a certain accession value (as populated in the uploaded field design file), use the dropdown menu to select a different accession. To view the distribution of all accessions, leave the accession as None.
  • To save the current graph view as an image, click Save As Image in the bottom left corner.

Graphical Statistics

To navigate to the map page, click on the Map Icon. Use the icon with three lines to open and close the data selection menu.

  • Populate the data selection menu with the Year, Experiment, Location, Population, Date, Platform, and Sensor you wish to view.
  • The map will automatically adjust to show the full orthomosaic generated for the parameters selected.
  • Use the dropdown menu to select the Trait Metric to view. After selecting, use the next dropdown menu to select the Genotype to view.
  • The rectangles formed in the population boundary step will show a range of colors based on the trait selected. Use the key at the bottom of the map to interpret the colors shown.

Map View Height Map View Veg

Query

To navigate to the query page, click on the Query Icon. Use the icon with three lines to open and close the data selection menu.

  • After selecting Year, Experiment, Location, and Population in the data selection menu, populate the Date, Platform, and Sensor dropdowns to select the data to query.
  • There are three options for image query available, with only one being used at a time:
    • Plot Numbers: Select from the dropdown menu the plot numbers whose images are to be queried.
    • Accessions: Select the unique accession IDs of the images to be queried.
    • Row / Column Pairs: Input Row / Column pairs (R, C) to select the images to be queried.
  • Click View Images to see the selected images to the right of the dropdown menus. Click Download to download the selected images as a .zip file.
  • Images shown on the page can be hovered over to see the unique accession ID and plot number of each.

Query Page