Display LoG transformed image in setup_puncta_analysis.ipynb
Motivation
One of the most challenging steps in the puncta segmentation protocol is optimization. I suspect this may be a result of the puncta detection and segmentation being based on the LoG-transformed images, but the images during selection of parameters are the original intensity images.
Pitch
Alongside the displayed images of the puncta signal, i propose a display of the LoG-transformed images when selecting Sigma parameters, puncta detection, and puncta segmentation.
Alternatives
I don't know if this would necessitate multiple images (one for each kernel used) or if there's a way to compile all of the relevant information into one transformed image. Perhaps during the Sigma parameter designation the notebook can show each kernel's transformation, and the following steps display the combined transformations.
Would it be possible to output the transformed images as a TIF during run_puncta_analysis.ipynb? This may help when trying to understand unexpected results.
Additional context
Perhaps the transformed images can go to the right of the original intensity image, and can also have the detected centers superimposed upon them.
🚀 Feature
Display LoG transformed image in setup_puncta_analysis.ipynb
Motivation
One of the most challenging steps in the puncta segmentation protocol is optimization. I suspect this may be a result of the puncta detection and segmentation being based on the LoG-transformed images, but the images during selection of parameters are the original intensity images.
Pitch
Alongside the displayed images of the puncta signal, i propose a display of the LoG-transformed images when selecting Sigma parameters, puncta detection, and puncta segmentation.
Alternatives
I don't know if this would necessitate multiple images (one for each kernel used) or if there's a way to compile all of the relevant information into one transformed image. Perhaps during the Sigma parameter designation the notebook can show each kernel's transformation, and the following steps display the combined transformations.
Would it be possible to output the transformed images as a TIF during run_puncta_analysis.ipynb? This may help when trying to understand unexpected results.
Additional context
Perhaps the transformed images can go to the right of the original intensity image, and can also have the detected centers superimposed upon them.