ykevu
commented
1 year ago Hi Megan,
I would suggest you reopen this issue at https://github.com/vanvalenlab/deepcell-tf/issues. This is the repo for DeepCell Label, the web application used for adding/editing labels to images, not for the DeepCell algorithms.
If you have questions about manually editing your DeepCell segmentation outputs with DeepCell Label, I would be happy to answer them, however.
Is your feature request related to a problem? Please describe. I am trying out using Mesmer for segmentation through the Bodenmiller steinbock/IMCRtools pipeline and applying it on human kidney tissue samples. I am finding that using the default training data for Mesmer is resulting in very small (1-2 pixel in size) debris being identified as nuclei. This happens both for cell segmentation and for nuclear segmentation. Looking at the source code available online (https://deepcell.readthedocs.io/en/latest/_modules/deepcell/applications/mesmer.html), I wondered whether you would recommend adjusting any of these parameters (ie nuclear radius) for this issue, or if you had another suggestion I could try? Is this a common issue?
Describe the solution you'd like Suggested alteration to source code or training data to use to improve inappropriate labeling of debris as nuclei.
Describe alternatives you've considered We previously segmented using Ilastik/CellProfiler, but are looking for a more streamlined approach -- and additionally the segmentation of true nuclei does appear more accurate in DeepCell than it does in our former approach.
Additional context Deepcell segmentation including many very small debris identified as cells/nuclei
Nuclear marker only