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James Ackman ackman678

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ackman678 /
Last active April 2, 2017 00:10
A poem by James Ackman dedicated to his sister Amy Rose, who passed away in Jan 2010
title author date
James B. Ackman
2010-01-28 01:31:00 -0800


The energy of life ebbs and flows between all and whom that surround us.
Boundless, it can be tamed but never controlled.

ackman678 / main.css
Created July 26, 2016 09:51
custom css mashup from jekyll base sass v3.1.6 and bootstrap-sass v3.3.6 for ackmanlab jekyll site
View main.css
table {
border-collapse: collapse;
border-spacing: 0; }
th {
padding: 0; }
* Reset some basic elements
ackman678 / 2016-07-12-Opencv3.1.0-dev-python-highgui-cmake.txt
Last active July 13, 2016 23:11
cmake config and output for successful compiling of opencv 3.1.0 on AWS ubuntu server 14.04 with anaconda python3.5 and GTK+2.x/highgui support
View 2016-07-12-Opencv3.1.0-dev-python-highgui-cmake.txt
ubuntu@ip-172-31-25-123:~/opencv/release$ cmake -DWITH_1394=OFF -DWITH_QT=OFF -DWITH_VTK=OFF -DCMAKE_INSTALL_PREFIX=/usr/local -DWITH_TBB=ON -DCMAKE_BUILD_TYPE=RELEASE -DBUILD_NEW_PYTHON_SUPPORT=ON -DCMAKE_INSTALL_PREFIX=$(python3 -c "import sys; print(sys.prefix)") -DPYTHON3_EXECUTABLE=$(which python3) -DPYTHON3_INCLUDE_DIR=$(python3 -c "from distutils.sysconfig import get_python_inc; print(get_python_inc())") -DPYTHON3_PACKAGES_PATH=$(python3 -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())") ..
-- The CXX compiler identification is GNU 4.8.4
-- The C compiler identification is GNU 4.8.4
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
ackman678 / addEvent_Calendar.applescript
Last active December 2, 2019 01:42
An add event to Calendar applescript.
View addEvent_Calendar.applescript
--James B. Ackman, 2008-02-06. Based on a script by Kevin Bradley at
set defCalendar to "Work"
--global ICactive
set theDate to short date string of (current date)
--Get event Summary
display dialog "Enter event name:" default answer " Appointment"
set eName to text returned of the result
--Get date
ackman678 / Rename_Labels_in_Results_Table.txt
Created April 25, 2014 20:35
A macro to rename roi labels (remove filename prefix) in an ImageJ results table. Script from [stackoverflow hint](
View Rename_Labels_in_Results_Table.txt
macro "Rename Labels in Results Table" {
for (i=0; i<nResults; i++) {
oldLabel = getResultLabel(i);
delimiter = indexOf(oldLabel, ":");
newLabel = substring(oldLabel, delimiter+1);
setResult("Label", i, newLabel);
ackman678 /
Last active October 18, 2017 15:53
An ImageJ macro to make a dF/F movie from a calcium imaging recording. Works best if file extension is changed to '.ijm' and saved in your ImageJ application folder at plugins/Macros/dFoFmovie-CatFullAutoSave.ijm
//dF/F image stack, James B. Ackman 2012-02-14, update 2014-04-18 13:55:00
// this macro can
// (1) Concatenate multiple image timeseries stacks (multiple tiff stacks) if nImages>1. Make the stacks are opened in order.
// (2) reduce an open image stack in half if halfsz==1 (default is halfsz==0)
// (3) create an average image over time (z-dimension)
// (4) calc dF/F image stack
// (5) Auto save the average image in original directory
// (6) Auto save an .avi movie in original directory
var name1;
ackman678 /
Last active April 6, 2016 18:14
Instructions on converting a multimarkdown manuscript with mmd bibtex cite-keys and graphics into a Microsoft Word document with BibDesk cite-keys and graphics.

Convert multimarkdown manuscript to Microsoft Word document

Here are directions for converting a markdown/multimarkdown formatted text manuscript into a Microsoft Word document (unfortunately still a preferred format for submission to many journals). These directions will focus on turning bibtex citekeys (if you are using BibDesk or similar for references and bibliography management) from the [#citekey] format in multimarkdown to the \cite{citekey} format for use with and to

This will use the Multimarkdown command line tool (mmd2odf) to create a flat open office document .fodt text file. Multimarkdown must be installed on your system. Alternatively pandoc can be used for this, but pandoc doesn't handle the nice multimarkdown table format as well and graphics can be messed up in resulting open office document .odt file.

Note on use of fodt files in OpenOffice:

>LibreOffice can open these Flat OpenDocument files by defaul

ackman678 /
Last active January 25, 2018 01:30
Brief command shell tutorial. Contains a few unix tips and tricks for working with and examining data files for science. A couple of the examples assume that the working environment is Mac OS X (e.g. pbcopy).
View github.css
body {
font-family: Helvetica, arial, sans-serif;
font-size: 14px;
line-height: 1.6;
padding-top: 10px;
padding-bottom: 10px;
background-color: white;
padding: 30px; }
body > *:first-child {
ackman678 / dFoverFmovie.txt
Last active May 23, 2018 03:34
An ImageJ macro to make a dF/F movie from a calcium imaging recording.Works best if file extension is changed to '.ijm' and saved in your ImageJ folder at plugins/Macros/dFoverFmovie.ijm
View dFoverFmovie.txt
//dF/F image stack, James B. Ackman 2012-02-14, update 2014-02-21 09:44:13
// this macro will (1) reduce an open image stack in half
// (2) create an average image in the z-dimension
// (3) calc dF/F image stack
// Uncomment the lines 21 run("Size..." ...) as well as the filenames at line 14,32 if you want to downsample the movie size
// To run without the autosave option, comment out the lines 62
// Comment out lines 41-58 if you don't want to auto adjust the contrast