psobolewskiPhD’s gists

psobolewskiPhD / tensorstore_labels_patches.py

Created May 16, 2024 16:27

painting patches of a large labels layer using tensorstore

	# %%
	# The idea behind this is to enable painting into a patch of a large
	# labels layer that is loaded multiscale into napari
	# By using tensorstore we can paint into a view of the array
	# in memory and then commit the painting to disc async.
	# This ends up being quite responsive and performant.
	# %%
	import numpy as np
	import napari
	import tensorstore as ts

psobolewskiPhD / points_scale1_n3d.py

Created April 8, 2024 22:27

script to setup point annotator test

	import napari
	import numpy as np

	from skimage import data
	from napari_threedee.annotators import PointAnnotator
	from napari_threedee.manipulators import RenderPlaneManipulator

	viewer = napari.Viewer()

	image_data = data.cells3d()[:,1,...] # just get the one channel

psobolewskiPhD / point_annotator_scale_bug.ipynb

Created April 8, 2024 21:40

napari-threedee point annotator when layer has scale

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psobolewskiPhD / toggle_blending_with_vis.py

Last active December 24, 2022 19:22

Keep Bottom-visible layer blending translucent

	import napari
	from skimage import data
	viewer = napari.Viewer()

	viewer.add_image(data.kidney(),
	colormap = ["I Blue", "I Purple", "I Orange"],
	channel_axis=3,
	rgb=False,
	blending= ["translucent_no_depth", "minimum", "minimum"]
	)

psobolewskiPhD / gist:6c32cb8e796c8cfb0bc2fb09ef66cee7

Created December 17, 2022 09:43

pip list for napari-dev

	Package Version Editable project location
	----------------------------- ------------------------------ -----------------------------------------------
	aicsimageio 4.9.2
	aicspylibczi 3.0.5
	aiohttp 3.8.3
	aiosignal 1.2.0
	alabaster 0.7.12
	app-model 0.1.2.dev3+gf9c9390.d20221114 /Users/piotrsobolewski/Dev/app-model
	appdirs 1.4.4
	appnope 0.1.3

psobolewskiPhD / gist:67f1df6c87844cd5d673b81f365cf1ab

Created December 17, 2022 09:41

npe2 list traceback

	npe2 list (napari-dev) ─╯
	╭────────────────────── Traceback (most recent call last) ───────────────────────╮
	│ /Users/piotrsobolewski/Dev/miniforge3/envs/napari-dev/lib/python3.10/site-pack │
	│ ages/npe2/cli.py:291 in list │
	│ │
	│ 288 │ │
	│ 289 │ pm = PluginManager.instance() │
	│ 290 │ pm.discover(include_npe1=True) │
	│ ❱ 291 │ pm.index_npe1_adapters() │
	│ 292 │ pm_dict = pm.dict(include={f.lstrip("!") for f in normed_fields}) │

psobolewskiPhD / torch-mps-cellpose.py

Created December 12, 2022 16:41

Test script for cellpose MPS branch

	# %%
	%env PYTORCH_ENABLE_MPS_FALLBACK=1
	# %%
	import numpy as np
	import time, os, sys
	from urllib.parse import urlparse
	import skimage.io
	import matplotlib.pyplot as plt
	import matplotlib as mpl
	%matplotlib inline

psobolewskiPhD / gist:8881d8cc7aa00b35ac3d00bb68ab00e2

Created December 2, 2022 11:40

Followup ChatGPT to fix bug in https://gist.github.com/psobolewskiPhD/17d2944bf7c37ea6c2179a5aae0bf640

	import numpy as np
	from skimage import io
	from skimage import filters
	from skimage import morphology
	from skimage import measure
	from skimage import exposure

	# Read the TIFF image
	img = io.imread('organoid.tiff')

psobolewskiPhD / gist:17d2944bf7c37ea6c2179a5aae0bf640

Created December 2, 2022 11:03

Python script generated by ChatGPT, as followup to https://twitter.com/psobolewskiphd/status/1598629093817417728?s=61&t=2DtG5heFpMkBdz1XxH6_iQ

	import numpy as np
	from skimage import io
	from skimage import filters
	from skimage import morphology
	from skimage import measure

	# Read the TIFF image
	img = io.imread('organoid.tiff')

	# Apply median filtering to remove noise

psobolewskiPhD / gist:098f6f31a4dc0fd60e7cc86b648de9b5

Created October 5, 2022 09:34

macOS crash report Translated Report (Full Report Below) (macOS 12.6, arm64)

	-------------------------------------
	Translated Report (Full Report Below)
	-------------------------------------

	Process: python3.10 [34952]
	Path: /Users/USER/*/python3.10
	Identifier: python3.10
	Version: ???
	Code Type: ARM-64 (Native)
	Parent Process: fish [31007]

Peter Sobolewski psobolewskiPhD