tobac

tobac copied to clipboard

Custom watershed function

1

Currently we use the watershed function from the scikit-image library (https://github.com/scikit-image/scikit-image/blob/v0.19.2/skimage/segmentation/_watershed.py#L95-L229) for segmentation. This is fast, because it uses a cython backend (https://github.com/scikit-image/scikit-image/blob/v0.19.2/skimage/segmentation/_watershed_cy.pyx) but inflexible for use cases such as...

w-k-jones

Fix floating point error in 2d/3d coordinate interpolation

1

Resolves #433. Clipping of hdim1/2 values to size of dimensions (or size + 1 for periodic coordinates) in `feature_location`, and extrapolation enabled for 2d/3d coordinates as with 1d coords. *...

w-k-jones

Floating point error in feature detection breaks interpn

8

It looks like there is a chance during the feature detection step for the identification of cells on boundary edges which result in hdim1 or hdim2 values slightly outside of...

travis-j-hahn

updated docstrings for n_min_threshold

2

Solves #427 * [x] Have you followed our guidelines in CONTRIBUTING.md? * [x] Have you self-reviewed your code and corrected any misspellings? * [x] Have you written documentation that is...

JuliaKukulies

Added missing test for get_spacings

1

This PR addresses #425 and adds a test for the get_spacings function. * [x] Have you followed our guidelines in CONTRIBUTING.md? * [x] Have you self-reviewed your code and corrected...

fziegner

`min_distance` doesn't work with 3D tracking where `dz` not constant

4

Reported to me by Yishi Hu from OU. When you use `min_distance` in feature detection with a non-constant `dz`, it fails as the coordinate interpolation takes place after `min_distance` is...

freemansw1

We updated `n_min_threshold` to support lists and dicts in v1.5.0, but didn't update the documentation. It would be nice to get this quick fix in before 1.5.4 comes out. *...

freemansw1

Add ability to add features to existing track without retracking

4

This new function (and its various support functions) is designed to allow the user to append a newly detected feature DataFrame to an existing set of tracks. This (should) work...

freemansw1

It seems that readthedocs is now putting a pesky warning on the documentation pages that are on `latest` by default (see screenshot). This isn't necessarily a bug, but this is...

freemansw1

* [x] Have you searched the issue tracker for the same problem? * [x] Have you checked if you're using the latest version? If not, which version are you using?...

fsenf