This PR updates SCDataFrame to enable cropped image-based output for .tiff files in order to better visualize single-cell information in context with quality control aspects already implemented within coSMicQC. Along the journey towards this work I found that we needed to extend pandas.DataFrame through SCDataFrame in order to effectively achieve the related outcomes. This in turn caused many more changes to the SCDataFrame class which may not look necessary but ultimately enable the use of the class within Jupyter contexts (while retaining existing functionality).
I've added an example notebook to help demonstrate the capabilities found within this PR. Within this example notebook I also implement the existing label_outliers function and show the plots to help ensure all existing functionality was not impacted by the new additions found here.
The changes here strive towards #33 by addressing #40 (we still will need to find segmentation data and add this to display).
Closes #40
What kind of change(s) are included?
[x] Feature (adds or updates new capabilities)
[ ] Bug fix (fixes an issue).
[ ] Enhancement (adds functionality).
[ ] Breaking change (these changes would cause existing functionality to not work as expected).
Checklist
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Description
This PR updates
SCDataFrame
to enable cropped image-based output for.tiff
files in order to better visualize single-cell information in context with quality control aspects already implemented withincoSMicQC
. Along the journey towards this work I found that we needed to extendpandas.DataFrame
throughSCDataFrame
in order to effectively achieve the related outcomes. This in turn caused many more changes to theSCDataFrame
class which may not look necessary but ultimately enable the use of the class within Jupyter contexts (while retaining existing functionality).I've added an example notebook to help demonstrate the capabilities found within this PR. Within this example notebook I also implement the existing
label_outliers
function and show the plots to help ensure all existing functionality was not impacted by the new additions found here.The changes here strive towards #33 by addressing #40 (we still will need to find segmentation data and add this to display).
Closes #40
What kind of change(s) are included?
Checklist
Please ensure that all boxes are checked before indicating that this pull request is ready for review.