raacampbell’s gists

raacampbell / switchEnclosureLights.m

Created July 3, 2025 12:02

Switches the lights of ScanImage microscope enclosures on and off

	function switchEnclosureLights()
	% Switches the lights of the microscope enclosure on and off
	%
	% function switchEnclosureLights()
	%
	% Purpose
	% Switches the microscope enclosure lights on and off. Uses the ScanImage ResourceStore
	% to communicate with the DAQ and cache the last state of the lights. The lights will
	% not be turned on when the PMTs are on. The PMTs can not be turned on when then lights
	% are on.

raacampbell / reg_two_fields.ipynb

Created June 18, 2024 07:01

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raacampbell / mouse_rectangle.m

Created March 12, 2024 13:41

Rectangle whose free corner follows the mouse cursor

	function mouse_rectangle
	% Make a rectangle that is anchored at one corner at the axis origin but follows
	% the mouse cursor at the other.
	%
	% Instructions
	% Run "mouse_rectangle" then move mouse cursor over the axes.
	%
	% Inputs
	% none
	%

raacampbell / bake.m

Last active February 15, 2024 10:42

bake with hack for re-acquiring slice with a different laser

	function sectionInd = bake(obj,varargin)
	% Runs an automated anatomy acquisition using the currently attached parameter file
	%
	% function BT.bake('Param1',val1,'Param2',val2,...)
	%
	%
	% Inputs (optional param/val pairs)
	% 'leaveLaserOn' - If true, the laser is not switched off when acquisition finishes.
	% This setting can also be supplied by setting BT.leaveLaserOn. If
	% not supplied, this built-in value is used.

raacampbell / scanBeamPathDiagram

Created July 31, 2023 15:41

Path of laser beam over a scanned area showing blanking

	function scanBeamPathDiagram
	% Generate a figure showing a scanned beam with scan and image field
	%
	% The path of a resonant-scanned focused beam over a sample. The beam moves
	% sinusoidally along the fast axis whilst being scanned up/down with a galvo.
	% The area over which the beam moves is known as the “scan field”. On the left and
	% right edges the beam slows and turns around. In these areas the potential for
	% photodamage is greatest, as the beam is travelling more slowly over the sample.
	% Thus the beam is “blanked” or disabled during these epochs. In a resonant scanning
	% microscope the beam is blanked about 30% of the time. The image field (red lines

raacampbell / basic_napari_example

Created May 9, 2022 13:58

Loading an image, adding layers, manipulating layers

	import napari
	import numpy as np
	from skimage import data
	from skimage.color import rgb2gray


	# Convert the astronaut image to a grayscale
	astro_im = rgb2gray(data.astronaut())

	# Display the astronaut image and also display its negative in a new layer

raacampbell / swipeTester.m

Last active February 28, 2022 20:01

Test swipe moves in BT

	function swipeTester

	% Test if BakingTray swipe moves are causing a failure

	% How large the swipe size should be.
	swipeSize = 4;

	% Pull in BT object
	evalin('base','clear ans') %Because it sometimes makes a copy of BT in ans when it fails
	hBT=BakingTray.getObject(true);

raacampbell / getGitInfo.m

Last active January 24, 2022 15:31 — forked from aleifer/getGitInfo.m

MATLAB getGitInfo: Get git repository hash, branch, and remote url in MATLAB

	function gitInfo=getGitInfo()
	% Get information about the Git repository in the current directory, including:
	% - branch name of the current Git Repo
	% -Git SHA1 HASH of the most recent commit
	% -url of corresponding remote repository, if one exists
	%
	% The function first checks to see if a .git/ directory is present. If so it
	% reads the .git/HEAD file to identify the branch name and then it looks up
	% the corresponding commit.
	%

raacampbell / python_for_MATLABists.txt

Created June 20, 2019 07:40

Stuff in Python that's notable to people coming from a MATLAB background


	## Multiple assignment
	a=b=c=0 # all have the same value

	a,b,c = 1,2,3 #a=1, b=2, c=3

	a,*b,c = 1,11,22,33,44,2 #b contains all numbers >10


	# Chaining comparison operators

raacampbell / polyN3_line.py

Created June 14, 2019 15:42

Fit a curve to a line in 3D

	#!/usr/local/bin/python3

	import numpy as np
	import scipy.linalg
	from mpl_toolkits.mplot3d import Axes3D
	import matplotlib.pyplot as plt

	# some 3-dim points
	n=20
	xx=np.linspace(-12,5,num=n)

Rob Campbell raacampbell