I have already installed the both plugins but don't know how to use them for pod analysis. Need help in that as i don't have programming background. Also can we use it for batch processing of images, in case i have more than 100 images?
2 Answers
Another approach per specially coded ImageJ-macro gives reasonable estimates of the widths and lengths of all pods in the sample image. You can access the macro code from here. Unzip the zip-archive and drop the file "plantPodDimensions.ijm" onto the ImageJ main window. Then open the sample image and run the macro. The estimated pod dimensions appear in a table.
Specimen [right to left] Mean Pod Width [cm] Pod Length [cm]
OHiI7_pod-1 0.70±0.11 23.6
OHiI7_pod-2 0.59±0.09 22.3
OHiI7_pod-3 0.64±0.05 20.7
OHiI7_pod-4 0.41±0.04 20.5
OHiI7_pod-5 0.66±0.07 22.9
OHiI7_pod-6 0.68±0.10 24.4
OHiI7_pod-7 0.60±0.07 20.5
Of course it couldn't be tested, if the macro works as expected for other images than the sample image.
With the download of the plugins come documents that explain the use of the plugins. Batch processing is possible, if the starting points of the traces are known or can somehow be determined by additional pre-processing steps (not trivial). Both plugins are macro-recordable. In any case, batch processing will require some macro code. For the use case in question I would recommend to perform the analyses via the GUI, not per batch processing. The coding of a suitable macro would take more time than the processing of 100+ images.
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