Fix Allen Notebook #692
Fix Allen Notebook #692
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Of note, the documentation in trackpy is wrong. The coordinates are emitted in (y, x) and (z, y, x). I verified by checking the coordinates of the maximum-valued spot in the imagestack and then finding the same value in the IntensityTable. |
ambrosejcarr
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FYI, tests were passing prior to rebase, so I believe this is probably clean/safe to land. I'll tag @dganguli for review for later, but we should get this in master and tested before he's back. |
notebooks/py/allen_smFISH.py
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| # EPY: END markdown | ||
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| # EPY: START code | ||
| primary_image.show_stack({Indices.CH.value: 0}); | ||
| _ = primary_image.show_stack({Indices.CH.value: 0, Indices.Z.value: 17}, rescale=True) |
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Done remember. Removed.
| clip = Filter.Clip(p_min=10, p_max=100, is_volume=False) | ||
| clip.run(primary_image, verbose=True, in_place=True) | ||
| # EPY: END code | ||
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| # EPY: START code | ||
| from showit import image |
| # image._show_spots(results, ax=plt.gca(), scale_radius=7); | ||
| # if max radius is 3, and mean intensity is about 0.006, and we can expect spots to have around pi*r^2 integrated intensity... | ||
| # try half-maximal radius * mean intensity | ||
| (np.pi * 1.5 ** 2) * 0.006 |
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Added explanation. Thanks for the catch.
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You likely will want to update .travis.yml as well. |
Fixes the Allen Notebook. Note that "use_test_data" doesn't seem to do anything?
The notebook still takes ~ 2.6GB of ram, presumably with a ceiling of + 1/3 when volumes are being manipulated. However, it's all starfish, and it runs.
Fixes #669