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Programs and iOS Reviews

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Igor Procedures and Bibdesk Templates

Igor procedures for Trapani zfish zphys analysis panel are now located on Amherst College's Gitlab: (please email Joe for access)

Igor Pro (by Wavemetrics) “is an extraordinarily powerful and extensible scientific graphing, data analysis, image processing and programming software tool for scientists and engineers...The IGOR scientific graphing and data analysis program has been in active development since its introduction on Macintosh in 1988.”

Procedure files () are hosted on Igor Exchange

**NEW** Solutions Panel

This procedure file that creates a simple panel for calculating the molarity, volume, or weight needed to make a stock solution given a molecules formula weight and two of the three parameters. A second calculator is available to solve for dilutions (M1•V1 = M2•V2) to make a working solution from a stock concentration.
Both calculators have the ability to change units (mg, g, ml, etc) via dropdown menus.
Compiling the procedure places a menu item in the Macros.

Line Scan Analysis

A procedure for generating kinetic profiles from analysis of intensity values from confocal line scans.
Sequential line scans are imported into 2D waves from either TIFF or Zeiss LSM* files.

Analysis options include:
  • choice of statistical test run on line scan data
  • ability to set inter-line scan-interval
  • stat values output to data table
  • creation of a graph and curve fit options
Running "Line Scan Analysis" from the Macros menu creates a panel (see screenshot). (* requires the LSMreader.pxp written by Stephen R Ikeda :

Brownian Motion Simulator
A Procedure File (BM_Simulator.ipf) for simulating a random walk and modeling Brownian Motion.

This procedure creates a series of displacements generated after a "particle" experiences a series of random molecular collisions. Each collision moves the particle a distance determined by its mean free path setting. After a defined number of collisions, the particle is at a new, random location and the distance between its starting location and final location is termed a "displacement". In the laboratory setting, this is equivalent to the displacement a particle undergoes in between two consecutive frames during imaging with a CCD camera. A series of these random displacements is then used to estimate Brownian Motion for a particle in 2-D space.
Compiling the procedure places a Menu item under Macros.

Lumencor SOLA light driver

The following procedure creates a small, simple panel for controlling a Lumencor SOLA light driver: This was created primarily to use with OS X as the company does not provide software for controlling the light source from a Mac.
 Including the procedure during compile adds an item called "Lumencor SOLA" in the /Macros menu item. Note:
The FTDI USB to Serial driver must be installed on the machine: 
The VDT2.xop procedure must be also be activated in Igor.

Fluorophore Excitation and Emission Spectra

The following Igor pxp file includes a panel for plotting the excitation and emission spectra of various fluorophores, including fluorescent chemicals (e.g., FM 1-43) or genetically encoded molecules (e.g., GFP). Includes the ability to overlay filter cube information (currently just FITC/EGFP and TRITC). Excitation and emission spectra are from Chroma.

Tone Generator Panel

This is a procedure file that creates a panel for controlling generation of an audio tone (played out of the computer speakers or headphone jack).
 Users can define frequency, duration, and whether the tone is repeated (as well as the delay between consecutive tones). Compiling the procedure places a menu item in the Macros.

BibDesk is a reference manager and bibliography editor. “Use BibDesk to edit and manage your bibliography and file your PDFs. It will keep track of both the bibliographic information and the associated files or web links for you. BibDesk’s services will simplify using your bibliography in other applications and are particularly well suited for LATEX users. BibDesk is developed as an open source project and available free of charge.”

UPDATE: PocketBib is a great iOS app that works with BibDesk libraries and Dropbox!

RTFD View Template (for displaying references within Bibdesk)

Save the file into the templates folder: /Users/username/Library/Application Support/BibDesk/Templates
Then within Bibdesk Preferences/Templates change the "Default RTFD Template" to this new file.
Then select this template from the preview window, as per picture.

RTFD Abstract Template (for copying citation info w/ abstract)

Save the file into the templates folder: /Users/username/Library/Application Support/BibDesk/Templates
Then within Bibdesk Preferences/Templates make a new rtfd General Template and link it to this new file.
Then under Bibdesk Preferences/Citation Behavior, set the “Format when holding Option key” to "Template" and select your new template file from the dropdown menu.


Apple App Reviews

Here's a video of me explaining use of an iPad for teaching and lecturing:
Cloud file storage and moving files to and from iOS devices

There are other options like Drive, Sugarsync, iCloud, etc... But my favorite is Dropbox. A great way to sync files to and from multiple computers, iPhones, and iPads. I pay for the 2 TB per year plan and keep all my files and data exclusively in the Dropbox cloud. When I get home, all files that I worked on during the day are synced to my laptop, iPhone, and iPad. If I'm away from home or work, I can access every file on my iPad (and iPhone), which is great for accessing or emailing a file to someone (or opening it within one of the apps listed below). If you work on a Mac, check out how to use symlinks or here.

Note taking; Drawing; PDF reading & markup

I have a premium account with Evernote and sync many, many things with Evernote, both on my desktop and iPad. I use the "Add to Evernote" plugin for Firefox to keep track of webpages. I use the ability to email to your private Evernote email address to send notes directly from other apps to make them searchable (Evernote servers scan handwritten text), and I use the in app syncability from Penultimate to sync notes from that Evernote owned app. I also have all my lab students keep their lab notebooks digitally using their own free Evernote account via sharing a Notebook with them. Also, the print option allows them to print their notebook out to take with them at the end of their time in the lab (thanks to Joe Burdo for this idea). 


Hands down the best PDF reader and editor out there. It syncs with Dropbox, WebDav, and many other cloud and server storage options. It also has a great engine for marking-up PDFs with handwriting. If you own an iPad you should have this app.

[backing up in Goodreader can be done via Dropbox, or wirelessly via a built-in wifi function]

Notetaker HD

This app is a powerful notetaking app on the iPad, BUT it is very outdated! There is a steep learning curve for using it. It can do most everything and has a very robust folder architecture for storing folders within folders etc. There is also a really neat template function that allows you to define the dimensions of a template note (I use this in order to make a note that is 1024x768, which works great when using the app as a whiteboard for projecting). You can also email your notes to Evernote.

 [backing up can be done by outputing your entire Notetaker HD file to dropbox or email]


UPDATE: Notability now syncs audio with your handwriting!! The best note taking app in my opinion. My favorite part about Notability is that you can record audio while taking notes, and if you switch to another app or lock the iPad it keeps on recording. The app backs up to iCloud and syncs with Dropbox, Google Drive, WebDAV and more.


Almost too powerful of a drawing app for day to day sketches. Supports multiple layers and infinite changes to many different types of drawing instruments. Output pictures to Dropbox or Photos as Photoshop files or JPG or transparent PNG. Quite nice, but almost too much.

**NOTE: I've been using Notability for a lot of my drawings, though it only exports to Dropbox as PDF, I've requested PNG and I am sure others have too. If you open the PDF on your mac and use Command+Option+4 key combination, you can take a screen shot that will save to your desktop as PNG. Or you can hold the Home button+Lock button on your iOS device and take a screen shot that will save into the Photos App as a PNG.

Reference and PDF Management

This app is a great solution for Mac users of BibDesk, an open-source reference management program. Together with DropBox, the app syncs to your BibDesk *.bib files and displays all their references and if the have attached PDFs, it will open them within the app. The best part is that if you then “open-in” the PDF in another app like GoodReader, you can mark the PDF up and then send it back to PocketBib, which then updates the PDF on Dropbox, which will then sync it with your mac--voila annotated PDFs synced across machines.


When used with either the "Dock to VGA adapter" or wirelessly with an AppleTV (see iOS Devices); Keynote is a great presentation app because it can show your upcoming slide on the iPad (similar to Presenter Tools on Powerpoint) while the audience views the current slide full screen. I use this as my primary lecturing platform and then app switch to Notetaker HD (see above) when I need a "whiteboard" since it allows for zoomed drawing on the iPad while displaying the page on the projector.

**note: Follow these guidelines for making Keynote presentations on your Mac that look best on your iPad.

**note: To get a movie to play in Keynote on the iPad, open it first in Quicktime and choose File>Export... from the top menu and change the Format drop-down menu to "iPod touch and iPhone 3GS" or equivalent option. Now, when you drag this movie into Keynote, it will embed into the Keynote file and be able to play on your iPad.**

Explain Everything

I haven't used this yet, but I've heard good things. Please send me an email if you've had positive experiences with this app.


This app allows you to markup a PDF that is displayed remotely via a desktop or laptop connected to a projector. Warning: I haven't used the app, but I like the concept.

Electronic textbooks

This is a not-so-great application for viewing what is essentially a low-res PDF of your textbook online and on an smart device (iPad, Kindle etc..) Many publishers work with this app/service, but it's really a pathetic attempt at an ebook (especially for 2013). See below for how publishers should be creating eBooks.


If you are fortunate enough to have your textbook integrated to work with this app, then lucky you! This is the way a textbook on the iPad (or other tablet) should be.


Anything written by hand on the iPad requires a good stylus and there are many out there, here are a few of my favorites:

Maglus Stylus
My current favorite. And I'm not alone:


This is a very nice stylus  (the RXII model). Over time the capacitative fabric looses its zing.

Adonit Jot Pro

It's noisy and not great for handwriting, but very precise for drawing with Procreate (see iOS App reviews).

Prof Gordon makes a stylus:
Link to article on his ACstylus
Joel Gordon, a physics professor emeritus at Amherst College, is making a $5 stylus! You can trim the foam tip to any shape you like, a useful feature if you'd rather use the stylus as a pointer, for writing, or for drawing. 100% of the proceeds go to the Friends of the Amherst Senior Center.
Adonit Writer (and Writer Plus)

A bluetooth keyboard can transform your iPad into a lean, mean typing machine (and it's much nicer than a laptop on an airplane to boot)

OLD SCHOOL: VGA Dock Connector

Standard dock connector to VGA adapter that allows an iPhone, iPod, or iPad to send video output via VGA.


A device that when hooked up to a projector allows wireless connection between the iPad (or other iOS device) and projector. There is nothing better than connecting wirelessly for a presentation.

**Check out the ATV Pro by Kanex. It allows you to easily connect an AppleTV to a VGA source (with audio output as well).

UPDATE! By combining an AppleTV, a Kanex ATV Pro adapter (for HDMI to VGA output), and an iPad with Verizon cellular data plan (for a Personal Hotspot, which the AppleTV can then join), you can setup AirPlay for wireless iPad output without needing a local network to join.