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Programs and iOS Reviews

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Igor Procedures and Bibdesk Templates

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

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 : http://www.igorexchange.com/project/LSMreader)

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:
http://lumencor.com/product/sola-light-engine/ 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: http://www.ftdichip.com/Drivers/VCP.htm 
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.

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iOS Reviews

File Syncing
SugarSync

Similar to Dropbox in many ways. It seems to manage syncing across multiple machines much better, including a built in app that allows you to decide whether you want to back up data to the cloud or just sync it across multiple machines. You can pick and choose different folders and share with many folks (even those without accounts). You get 5 GB free and then there are multiple paid data plans. I use Dropbox over SugarSync primarily because Dropbox is integrated into many more Apps.

Dropbox

A great way to sync files to and from multiple computers, iPhones, and iPads. I pay for the 100 GB per year plan and keep all my files and data exclusively in the cloud. When I get home, all files that I worked on during the day are synced to my home computer. 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 and PDF reading
Evernote

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 Notetaker HD to make them searchable (Evernote servers scan handwritten text), and I use the in app syncability from Penultimate to sync notes from that app. I also have all my lab students keep the lab notebooks digitally via their own free Evernote account (Notebooks can be shared), 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). 

GoodReader

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 is by far the most powerful notetaking app on the iPad. There is a steep learning curve for using it, but 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]

Notability

UPDATE: Notability now syncs audio with your handwriting!! Probably the best note taking app. 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 and exports to Dropbox and notes can be restored if you purchase a new iPad.

Byword

This app is available on the Mac and iPhone and iPad, which is convenient for working on your notes across platforms and having your notes in sync automatically. The best part is it is simple and has Dropbox integration, so you are not tied to iCloud as your only cloud sync option (like the default Notes app that as of OS X 10.8 is now available on the Mac).

UPad

This app is has gotten a lot better with recent updates. You can resize drawings (like InkFlow). It syncs with many services including Evernote. It exports as PDFs or PNGs. There is a lot to like about this app!

Reference and PDF Management
PocketBib

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.

Drawing (the following apps don't have a "zoom" feature so they don't work well for handwritten notes)
Penultimate

Really nice app for drawing. Drawings can be synced to Dropbox and Evernote directly from within the App.

PAPER

My favorite app for drawing, plus if you save a picture it can have a transparent background, which is really nice for Powerpoint or Keynote slides.

procreate

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.

Presenting
Keynote

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.

AirSketch

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
CourseSmart

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.

Inkling

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.

Stylus

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: http://www.theverge.com/products/maglus/5593

iFaraday

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.

Keyboards
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)

Projecting
OLD SCHOOL: VGA Dock Connector

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

NEW SCHOOL: AppleTV

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.