FelixChihTing

Hi Matt @mfigdore @tathey1 @bvarjavand , I'm testing `connected_threshold` in [adaptive_thresh.py](https://github.com/neurodata/brainlit/blob/develop/brainlit/algorithms/generate_fragments/adaptive_thresh.py) with a simple image as input: `img = np.array([[[100, 250], [800, 300]], [[1200, 2000], [3000, 2500]]])` and a seed...

@mfigdore I got the same error after changing from `(1,0,1)` to `[(1,0,1)]`.

@mfigdore the tutorial is out of date, some files are moved, e.g., `NeuroglancerSession` is now in `session.py`

@mfigdore currently only the following block in the [tutorial](https://github.com/neurodata/brainlit/blob/develop/docs/notebooks/algorithms/tutorial_notebook_adaptive_thresh.ipynb) is working: `from skimage.data import astronaut` `# create the viewer and display the image` `viewer = napari.view_image(astronaut(), rgb=True)`

I believe it's an [issue of SimpleITK](https://github.com/SimpleITK/SimpleITK/issues/1098).

@mfigdore the proposed solution does not fix the problem in my case

> @FelixChihTing Please see #226 which I believe will address the error. @mfigdore Great! that resolve the problem with `sitk.BinaryDilate`. Other than that, when I run `connected_threshold` with the following...

> @FelixChihTing > Should be `labels = connected_threshold(img, [(1,0,1)] )` Ohh, this works!! Thank you!

Hi @mfigdore @tathey1 , how is the `sigma` in [fast_marching_seg](https://github.com/neurodata/brainlit/blob/develop/brainlit/algorithms/generate_fragments/adaptive_thresh.py#L93) used in calculating the labels? I tried to input a 2D Gaussian image with standard deviation of 3 (left), and...

@tathey1 When I tried to segment a simple image as below, level_set_seg doesn't work correctly:  ``` img = np.zeros((15,15)) for x in range(0,16): for y in range(0,16): if x...