Thomas Athey

Writing Skeleton Question

8

Hi, I'm having issues creating skeleton objects locally using cloud-volume that can be seen in neuroglancer. Take this toy code: ``` from cloudvolume import CloudVolume, Skeleton import numpy as np...

Should Microsoft Azure be Supported?

7

Is Azure an option for storing precomputed data with cloud-volume? I see options for Google and Amazon but cannot find anything in the documentation about Azure.

Make NeuronTrace coordinate units more clear

1

Neuron trace coordinates typically come in one of two coordinate systems: physical (e.g. microns) or voxel (e.g. coordinates relative to corner of image, in units of voxels). Cloudvolume handles this...

fix warnings in pytests

5

running pytests raises various warnings (e.g. ndimage.morphology is deprecated), lets update the code to solve these warnings.

get pytest-qt to work on circleci

2

It would be great to uncomment the test [here](https://github.com/neurodata/brainlit/blob/develop/brainlit/napari_viterbrain/tests/test_plugin.py)

Checks don't have access to AWS permissions in PR's from forks

3

I tested two trivial PR's, one from a [fork](https://github.com/neurodata/brainlit/pull/341) where I got an AWS error, and one from a [branch](https://github.com/neurodata/brainlit/pull/342) where there was no error. Is it possible to allow...

tutorial [here](https://circleci.com/docs/2.0/parallelism-faster-jobs/) i started a pr [here](https://github.com/neurodata/brainlit/pull/328), but the tests still need to be split across the different containers. Currently (I believe) all 4 containers are running all the tests.

Update config.yml

1

https://circleci.com/docs/2.0/parallelism-faster-jobs/

Simplify compute_bounds function

5

There is a function that, given a component in a segmentation, computes the bounding box with a certain padding ([here](https://github.com/neurodata/brainlit/blob/bc4e388485dbf6cbf0933dbf01e3b4299794e564/brainlit/algorithms/connect_fragments/dynamic_programming_viterbi2.py#L249)). However this can be simplified by utilizing the [regionprops](https://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.regionprops) method...