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Genevieve Buckley GenevieveBuckley

  • Monash University
  • Melbourne
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View distributed-skeleton-analysis.ipynb
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View slices_from_chunks_overlap.py
# Proposed slices_from_chunks_overlap function
# Mofified from slices_from_chunks from dask.array.core
from itertools import product
from dask.array.slicing import cached_cumsum
def slices_from_chunks_overlap(chunks, depth=1):
"""Translate chunks tuple to a set of slices in product order
depth : int
@GenevieveBuckley
GenevieveBuckley / install_cupy_9.0.0b3.txt
Created Mar 15, 2021
How to install the beta version of Cupy 9.0.0
View install_cupy_9.0.0b3.txt
conda install -c conda-forge/label/cupy_rc cudatoolkit=11.2 cupy=9.0.0b3
@GenevieveBuckley
GenevieveBuckley / cellprofiler-environment-dev-ubuntu-20-04.yml
Created Feb 11, 2021
CellProfiler development conda environment export
View cellprofiler-environment-dev-ubuntu-20-04.yml
name: cellprofiler-dev
channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- alsa-lib=1.2.3=h516909a_0
- atk-1.0=2.36.0=h3371d22_4
- brotlipy=0.7.0=py38h497a2fe_1001
@GenevieveBuckley
GenevieveBuckley / cellprofiler-dev-installation-ubuntu-20-04.md
Last active Feb 11, 2021
CellProfiler development installation on Ubuntu 20.04
View cellprofiler-dev-installation-ubuntu-20-04.md

CellProfiler development installation on Ubuntu 20.04

Guide created February 2021

1. Install dependencies

Install these dependencies

sudo apt update
sudo apt -y upgrade
sudo apt install -y make gcc build-essential libgtk-3-dev
sudo apt-get install -y python3-pip openjdk-11-jdk-headless default-libmysqlclient-dev libnotify-dev libsdl2-dev
@GenevieveBuckley
GenevieveBuckley / restart-and-run-all.ipynb
Created Nov 10, 2020
Jupyter notebook restart and run all
View restart-and-run-all.ipynb
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@GenevieveBuckley
GenevieveBuckley / example-images.txt
Last active Oct 8, 2020
worm demo for napari affine transforms
View example-images.txt
Example images used can be downloaded from here: https://github.com/DeMarcoLab/correlateim/tree/master/data
View conda_compare.py
#!/usr/bin/env python3
"""
quicky script that compares two conda environments
can be handy for debugging differences between two environments
This could be made much cleaner and more flexible -- but it does the job.
Please let me know if you extend or improve it.
@GenevieveBuckley
GenevieveBuckley / pip_install
Created Sep 28, 2020 — forked from chrisRedwine/pip_install
Pip install a specific github repo tag or branch
View pip_install
# From https://coderwall.com/p/-wbo5q/pip-install-a-specific-github-repo-tag-or-branch
pip install -e git://github.com/{ username }/{ reponame }.git@{ tag name }#egg={ desired egg name }
@GenevieveBuckley
GenevieveBuckley / pyconlineau-beeware-briefcase-android
Created Sep 6, 2020
Notes from pyconline 2020 beeware sprints - briefcase on android
View pyconlineau-beeware-briefcase-android
briefcase android project
phone MUST be in file transfer mode
Must wait for the computer to recognise that the phone has been plugged in
Must allow USB debugging
https://pastebin.com/0xpejQPB
Traceback (most recent call last):
File "/home/xero/.virtualenvs/beeware-venv/bin/briefcase", line 8, in <module>