With the experiment board you can manage your experiments, by either creating new ones or stop running experiments. Creating new experiments involves telling PlantEye how to interpret your platform, and assigning plants (genotype and treatment information) to specific locations on your platform.
Table of Contents
- Setting up Experiments
- Step 1 | Selecting Blocks
- Step 2 | Configure selected blocks
- Step 3 | Experiment Design
- Step 4 | Start
Setting up Experiments
Setting up an experiment is one of the most important steps in the usage of HortControl and is done using the Experiment board. Here you can define how your field setup looks and which plants (genotype x treatment) are assigned to each location in your field.
During the experiment setup you define the connection between the physical world and the biological world so that data transfer from sensor to plant can occur.
To create and setup a new experiment select the Create module in the left sidebar. You should see the block layout of your platform in the center of HortControl, with a step wizard on top. Your platform is generally divided in multiple available (green) and unavailable (gray) blocks to which a number or barcode is assigned. Blocks can be unavailable when they are in use by another experiment. The screenshot below shows an example for what you should see.
Creating a new experiment involves four steps that have to be completed chronologically:
- Step 1: Here you reserve available blocks for your new experiment.
- Step 2: Lets you design your units inside a block
- Step 3: Assign your plants to a physical location
- Step 4: Summary of your experiment and finishing it up by giving a name
Step 1 | Selecting Blocks
Each experiment is defined for a selection of blocks. Whenever a Phenospex product collects data, HortControl will assign it to the corresponding plant as defined by it's physical coordinates (block x unit). Therefore, the first step in creating an experiment is selecting the blocks for it. If a block is in use by another experiment and you want to use it for a new experiment you have to stop
the old experiment first. A block will be green in the view if it’s free and can be used for new experiments and gray if it is still used by an active experiment.
To select the blocks for your experiment click and drag a rectangle around the blocks that you would like to select. Press the CTRL key and click and drag to add blocks to your selection or press the SHIFT key to remove them. You will see that the cursor will change into a + or - symbol if any of these keys are pressed. Selected blocks will be highlighted yellow as shown in the screenshot below.
When you have selected all blocks you wanted for your new experiment, you can proceed to step 2 using the wizard bar at the top.
Step 2 | Configure selected blocks
The next step is to further subdivide or split the selected blocks into units, which reflect the exact location of your plant in the platform. A list of predefined block layouts is made available in the Block layout drop-down. The selected splitting configuration will be visualized on the right hand side, together with the parameters used for splitting the block into units. You can always consult the question mark in the top left corner if you are not confident what to do.
If you want to arrange your plants differently than any layout that is provided, you can still create your own layout. For a detailed explanation about the block splitting settings and creating a new layout you are invited to consult the Create Block Configuration
Besides the block splitting layout, there are other block settings that need to be defined as well:
- Barcode height defines the height of the physical metal barcodes on the platform (if used) so that scanner coordinates can be converted to your platform coordinates.
- Pot height is used to remove any background and correctly compute plant height.
- Crop Radius can be used of you want a circular mask on your rectangular unit.
- Split configuration defines the splitting algorithm, and is rectangular by default. There are also hexagonal splitting methods available on request.
If you are ready with your block configuration, it is time to assign plants to the newly created units for your experiment.
Step 3 | Experiment Design
This is the step where you ultimately define the connection between the physical and biological world of your experiment. Here you can assign plant information (genotype x treatment) or metadata to your newly created units.
When you proceed to step 3 you will see that initially all selected blocks are yellow. Yellow indicates that not all metadata for these blocks was added. There are two ways to link metadata to your newly created units, you can choose to do it manually through the interface or by means of file upload.
For manually assigning plant information to your units, click on any yellow block to open a modal window that shows the block with all the units inside. In this modal window you can now assign a plant to each unit by defining its genotype and treatment. To do that, select one or multiple units by clicking and dragging a rectangle around them. Use CTRL or SHIFT to add or remove units from the current selection. After you made your selection, select the genotype or treatment you want and click the update genotype / treatment button. You will see that the color of the blocks will switch and a legend above the block will indicate all used genotypes and treatments. If you wish to apply this layout of treatment and genotype to all blocks in the experiment you can use the Copy genotype/treatment layout to all blocks button.
The other way of assigning metadata is by uploading a metadata file that contains the link between platform coordinates and plant information. This method will especially prove useful for bigger platforms/experiments. Under the download menu of the settings bar on the right hand side you can download such a file by pressing the Metadata button. You will get a CSV template that is prefilled with all block and unit information and has two empty columns that define treatment and genotype. Simply fill out this table either manually or by importing the data from your LIMS system. After that, open the settings bar again and this time under upload menu use the Metadata button to apply this layout to the entire experiment.
Either way, when all meta information was added correctly, you will see that all blocks turned green and the last step in the step bar will be enabled. Proceed to the last step.
Step 4 | Start
In the last step you see an overview of the number of blocks and units you intend to use in your experiment as well as the number of sample groups (unique combinations of genotype and treatment) and range of sample size (range of units assigned to the sample groups) that will be used. This is a last check for you to see if your experimental setup really fits your intended experimental design. Do you end up with the envisioned number of plants, sample groups, and sample size? If so, you only need to provide a name for your new experiment and start it! The experiment will start and you can start to check the incoming data.
Stop a running Experiment
To stop a running experiment open the Experiment Board. In the Experiment Board select the Stop Experiment view. You should see a visualization of your platform on the Canvas. All blocks should be color coded as in the example below showing what experiment is currently running on these blocks.
To stop any of the experiments either click on one of the blocks that belong to the experiment or use the drop-down at the top. If you start typing the experiment name that you want to stop the drop-down will directly filter to all experiments that contain the string you are typing. Either way after you have selected the experiment to stop the blocks of this experiment will be highlighted as in the screenshot below.
If you are sure that this is the experiment you wish to stop use the stop button next to the drop-down. Please be aware that stopping an experiment can not be undone. Only stop if you are certain that you wish to stop the experiment.