Closed K-Meech closed 5 months ago
I've had a look at some of the plugins and have some thoughts:
napari-aicsimageio
Has a large suite of tools for doing the sorts of operations we're interested in (Gaussian blur, thresholding, etc.)
Easy to install using pip (although I don't have an M1 Mac so can't test that out):
python -m pip install napari-segment-blobs-and-things-with-membranes
Actually provides a long list of plugins (available via Plugins > napari-segment-blobs-and-things-with-membranes > <plugin list>
)
Using some of napari's builtin data (File > Open sample > napari builtins > Human mitosis
), can label cells using the following workflow (each step is the name a separate plugin from the above list):
gaussian blur
threshold otsu
split touching objects
connected component labelling
manually split labels / manually merge labels
Similar to napari-segment-blobs-and-things-with-membranes
- has a large suite of tools for doing the sorts of operations we're interested in
Easy to install using pip:
python -m pip install napari-simpleitk-image-processing
this also provides a long list of plugins (available via Plugins > napari-simpleitk-image-processing > <plugin list>
)
Using the same builtin data (Human mitosis
), can label cells and calculate statistics using the following workflow (again each step is the name a separate plugin from the above list):
gaussian blur
theshold otsu
connected component labelling
label statistics
napari-segment-blobs-and-things-with-membranes
and napari-simpleitk-image-processing
are the most promising in terms of being easy to use and having the functionality we need.
In differences between the two:
napari-segment-blobs-and-things-with-membranes
has a tool to split touching objects before the segmentation step, and another to manually relabel datanapari-simpleitk-image-processing
can calculate some simple cell statistics. Plus, the connected component labelling seems to perform slightly better compared to napari-segment-blobs-and-things-with-membranes
(with fewer neighbouring cells being incorrectly connected)So we might want to use both napari-segment-blobs-and-things-with-membranes
and napari-simpleitk-image-processing
?
Thanks @p-j-smith - this is a great overview! Seems like napari-segment-blobs-and-things-with-membranes
and napari-simpleitk-image-processing
should cover everything we need for day 2.
I'll close this issue now, as all episodes that use these napari plugins are merged
For day 2, we'll need Napari plugins that can do basic operations like: image histograms, gaussian blur, thresholding, connected components, opening/closing
Some options to try out:
Definition of done