For the following steps require an annotation that highlights the plate area together with a physical pixel size. J-AST provides an automated operation that attempts to find the plate and then calibrates the pixel size.
To run the operation, select all images and go to Process > Plate > Auto-detect plate.
Please ensure that the plate diameter is correctly set up. Then start the run by clicking OK.
Note: depending on the server/computer capabilities and number of images to process this process can take multiple minutes.
Tip: if the detection fails, you can manually segment the plate or apply fixes. The pixel size calibration can be run independently by executing the Calibrate pixel size by plate operation. You can also put in the pixel size manually.
For DDAs you will need to find the disk. We provide multiple approaches (v1/v2/v3) that have different strengths and weaknesses depending on the image properties.
For the test data set the Auto-detect DDA disk (v1) operation works well.
The DDA disks should be now correctly detected.
The detection of the E-Test strips is handled through an operation Auto-detect ETest strip (v1).
By default the operation assumes that the aspect ratio of the strip is approximately 11 and that strips have a white outline. If you apply the operation on a complete data set, adapt the settings accordingly.
The detection of the E-Test strip is a non-trivial operation that relies on the algorithm finding the two parallel long sides of the strip and limiting the vertical area by finding the smaller sides. Depending on the image contrast, noise levels, and artifacts this operation might fail to produce a satisfactory outcome
In the next tutorial we will explain how to do a manual segmentation directly within J-AST.