MVP for morpohology module

[timtreis]

MRE:

import squidpy as sq
import spatialdata as sd
from spatialdata.datasets import raccoon
import spatialdata_plot
from scipy.stats import entropy

sdata = raccoon()

def my_func(regionmask, intensity_image):
    
    masked_values = intensity_image[regionmask]
    histogram, bin_edges = np.histogram(masked_values, bins=256, range=(0, 255))
    probabilities = histogram / np.sum(histogram)

    return entropy(probabilities, base=2)

sq.im.quantify_morphology(
    sdata,
    label="segmentation",
    image="raccoon",
    methods=["area", "perimeter", "circularity", "intensity_mean", my_func],
    split_by_channels=True,
)

Notes

• circularity is a non-skimage method but internal method (we need a library of those, can "steal" from CellProfiler + X)
• my_func is an external method that gets fed to skimage.measure.regionprops. We need to provide doc on how to make such method. They take in a mask of the respective cell as well as a (potentially multi-channel) intensity image (both np.ndarrays).
• add back to adata instead, align with rest of codebase
• now thing of how to integrate custom callables that are external to the codebase, f.e. huggingface models
• Needs to respect transformations & deal with different scales
• Needs notebook in squidpy-notebooks

From discussion on 2024-08-13

• Workstreams
  • 1. "baseline" regionprops: what skimage has natively as functions, can query by string
  • 2. "non-baseline" regionprops: other metrics we can "steal" from CellProfiler etc and make available by string internally
    • f.e. take math from https://github.com/CellProfiler/CellProfiler/blob/main/src/frontend/cellprofiler/modules/measuregranularity.py#L432
  • 3. feed in methods that take in mask / intensity image
  • 4. test performance of regionprops on actual data - does it work at scale at all?
    • if not, can we hijack the method and parallelize across chunks (parallel io) and collect
    • can we lazy-compute? dask?
  • 5. respect transformations and datatree "zoom" - which matches, what does the user want?
  • 6. my_func wrapper for model inference, f.e. from some HF-model?
    • download model etc?
    • they might require specific resolution, might have to scale all cells because area contains info

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 20.33898% with 47 lines in your changes missing coverage. Please review.

Project coverage is 69.52%. Comparing base (4a632d6) to head (bbecec3). Report is 5 commits behind head on main.

Files	Patch %	Lines
src/squidpy/im/_feature.py	20.33%	47 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #866      +/-   ##
==========================================
- Coverage   69.99%   69.52%   -0.47%     
==========================================
  Files          39       39              
  Lines        5532     5667     +135     
  Branches     1037     1063      +26     
==========================================
+ Hits         3872     3940      +68     
- Misses       1367     1429      +62     
- Partials      293      298       +5     

Files	Coverage Δ
src/squidpy/im/_feature.py	51.81% <20.33%> (-37.08%)	:arrow_down:

... and 2 files with indirect coverage changes

[npeschke]

I had to remove the code that called the label function from skimage as it was creating additional labels that we cannot trace back to the original labels.

[timtreis]

Superseded by https://github.com/scverse/squidpy/pull/982