Use case example¶

Create a folder for the result. We will create a new folder on the desktop called mb_results.
Open the Ananconda prompt and activate your macrobot environment if you are not already there.

conda activate macrobot

source path (-s) - the path with the images coming from the Macrobot hardware system
destination path (-d) - the path to store the results
pathogen (-p) - which pathogen to predict (“mildew” or “rust”)

For a test case we will use a test image set which will be automatically downloaded by the start of the software. To tell the software to use the test images, we will enter “test_images” for the source path -s argument
Start the software with the following command (adapt the destination path):

mb -s test_images -d C:\Users\name\Desktop\mb_results\ -p mildew

A csv file with the predicted values per leaf
A report html file in folder report which allows and easy control over the pipeline.
Images created by the software (white=pathogen, red=leaf detection, black=background)

If you want to use a real world experiments, make sure to provide the following folder structure with five images per plate:

my_folder

├── experiment1

│ ├── dai

└── plateID1

└── plateID1_backlight.tif
└── plateID1_green.tif
└── plateID1_blue.tif
└── plateID1_red.tif
└── plateID1_uvs.tif

├── experiment2

│ ├── dai

└── plateID2

└── plateID2_backlight.tif
└── plateID2_green.tif
└── plateID2_blue.tif
└── plateID2_red.tif
└── plateID2_uvs.tif

macrobot