Using PlantCV pcv.segment_image_series and pcv.create_labels to do image analysis

[ariaf7]

Hello! I am working with PlantCV to do image analysis of lettuce plants. I want to use the output from pcv.segment_image_series to analyze the shape and color of each of my lettuce plants. They overlap, which is why I am using pcv.segment_image_series in the first place. Here are the functions I am trying to use to do my analysis:

shape_img = pcv.analyze.size(img=img, **labeled_mask=labeled_mask**, n_labels=18)

shape_img = pcv.analyze.color(rgb_img=img, labeled_mask=labeled_mask, n_labels=18, colorspaces="RGB")

I know I need to use some sort of labeled_mask, num_plants = pcv.create_labels(mask=th_fill, rois=rois, roi_type="partial") for the labeled mask. However, I want to use the output from the pcv.segment_image_series function because it takes care of the overlap, while pcv.create_labels does not. And I can't use my output from the pcv.segment_image_series as input for pcv.create_labels or shape_img because the output isn't the right type. Sorry for not being very clear, I have very limited experience with PlantCV. I am not using the most recent version of PlantCV because I do not know how to update it as well. What do you all recommend?

[HaleySchuhl]

Hi @ariaf7 thanks for opening this issue. It has been brought up recently that the pcv.segment_image_series was a bit overlooked while we were updating the way PlantCV handles multi-object analysis in v4. This is something we're looking to address soon. In the meanwhile, here's how I was able to work around it. For more detail upstream of these steps, also see this GitHub issue.

...
analysis_image = pcv.segment_image_series(imgs_paths=paths_to_imgs_list, masks_paths=paths_to_masks_list, rois=valid_rois, save_labels=True, ksize=3)

lbl_mask = analysis_image[:,:,1]
shape_img = pcv.analyze.size(img=img, labeled_mask=lbl_mask, n_labels=20)
rgb_plot = pcv.analyze.color(rgb_img=img, labeled_mask=lbl_mask, n_labels=20, colorspaces="RGB")

Regarding updating your version of PlantCV, please refer to our updating doc page to see the recommendation depending on how you installed it. Please let us know if this helps.