Ruben Verweij rbnvrw

See the Python notebook for the code. If you scroll down all the way down, you see an example of the last frame in a tracked, cropped and sped-up video. Features:

Convert an ND2 movie into avi/mp4/mov/wmv format
Add a scalebar of your choice to the movie
Speed-up the movie by a certain factor
With a csv file containing (frame,x,y,r,particle) columns: overlay the trajectories, particle number, circle of tracked radius

Scalebar with background

To change the backgroundcolor, adjust the scalebgcolor variable to use the desired color. Add the following code to your preamble:

\usepackage{tikz}
\usepackage[usenames, dvipsnames]{color}
\definecolor{scalebgcolor}{rgb}{0.08,0.52,0.80}

Framed equations

\usepackage{empheq}
\usepackage[many]{tcolorbox}

\tcbset{
  highlight math style={
    enhanced,
    colframe=black,
 colback=white,

	#!/bin/bash

	# input file
	INFILE=thesis.pdf

	# output file
	OUTFILE=thesis_compressed.pdf

	# /printer compresses to ~300 DPI, various optimizations
	# -dPrinted=false preserves PDF hyperlinks

	sudo dnf install -y ruby ruby-devel lua lua-devel luajit \
	luajit-devel ctags git python python-devel \
	python3 python3-devel tcl-devel \
	perl perl-devel perl-ExtUtils-ParseXS \
	perl-ExtUtils-XSpp perl-ExtUtils-CBuilder \
	perl-ExtUtils-Embed
	# symlink xsubpp (perl) from /usr/bin to the perl dir
	sudo ln -s /usr/bin/xsubpp /usr/share/perl5/ExtUtils/xsubpp
	git clone https://github.com/vim/vim.git vim-src
	cd vim-src

	function! s:tablePandoc() range
	exe "'<,'>Tabularize /\|"
	let hsepline= substitute(getline("."),'[^\|]','-','g')
	exe "norm! o" . hsepline
	exe "'<,'>s/-\|/ \|/g"
	exe "'<,'>s/\|-/\| /g"
	exe "'<,'>s/^\| \\\|\\s*\|$\\\|\|//g"
	exe "'<,'>!pandoc -f markdown -t rst"
	endfunction
	command! -range=% TablePandoc :call <SID>tablePandoc()

	" move vertically by visual line
	nnoremap j gj
	nnoremap k gk

	" highlight just the 81st column of wide lines... (Damian Conway)
	highlight ColorColumn ctermbg=magenta
	call matchadd('ColorColumn', '\%81v', 100)

	" Enable code folding
	set foldenable

	#BIMP 1.16
	#MANIPULATION SET DEFINITION

	[USERDEF0]
	procedure=plug-in-despeckle
	num_params=7
	PARAM0=1
	PARAM1=NOT_USED
	PARAM2=NOT_USED
	PARAM3=2

	from igraph import *
	import numpy as np

	# Create the graph
	vertices = [i for i in range(7)]
	edges = [(0,2),(0,1),(0,3),(1,0),(1,2),(1,3),(2,0),(2,1),(2,3),(3,0),(3,1),(3,2),(2,4),(4,5),(4,6),(5,4),(5,6),(6,4),(6,5)]

	g = Graph(vertex_attrs={"label":vertices}, edges=edges, directed=True)

	visual_style = {}