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split up context documentation and clarify
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HaleySchuhl committed Jul 29, 2024
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7 changes: 5 additions & 2 deletions docs/Points.md
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Expand Up @@ -36,7 +36,7 @@ import plantcv.plantcv as pcv
import plantcv.annotate as an

# Create an instance of the Points class
marker = an.Points(img=img, figsize=(12,6))
marker = an.Points(img=img, figsize=(12,6), label='default')

# Click on the plotted image to collect coordinates

Expand All @@ -62,7 +62,10 @@ Using [Jupyter Notebooks](https://plantcv.readthedocs.io/en/stable/jupyter/) it
- num - The number of unique objects in the `corrected_mask`.

- **Context:**
- Filters objects from the `bin_mask` if they do not overlap with an annotation in the `Points` class instance. Also adds a labeled pixel to the corrected mask if an object cannot be resolved for any annotations. Also returns the number of unique objects in the `corrected_mask` which is useful for downstream analysis.
- Filters objects from the `bin_mask` if they do not overlap with an annotation in the `Points` class instance.
- Adds a labeled pixel to the corrected mask if an object cannot be resolved for any annotations (false negatives can be counted but cannot have their size measured downstream).
- Returns the number of unique objects in the `corrected_mask` which is useful for downstream analysis.
- Debug image is a colorized representation of the labeled mask. The "unresolved" annotation replicates are plotted with a radius of `pcv.params.line_thickness` (default = 5).

- **Example use:**
- Remove noise from a microscopy image that is otherwise difficult to filter out with traditional computer vision
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