Another blog added
Posted in Software
Xcorr has some nice posts on coding, Plexon systems, analysis, and whatnot. It was just added to the Recommended Blogs section on the right. Some example posts:
A Plexon C++ API on 64-bit Linux…
Category: Software
Data’s killer app
Posted in Software
On the topic of the recent app post, I’ve been thinking about an old blog post from Peter Keane. The of his post is, “What is Data’s Killer App?” In it, he pondered the problem of data management.
After a not entirely apt analogy to HTML, Keane suggested that there is no killer app…
Apps
Posted in Software
You probably caught the article about the group who runs their laser-trapping experiments using an app they wrote for iOS on the iPad. This sparked a commentary about apps in science. What about some other apps for handheld and tablet computing?
Reference organization
In general, when it comes to…
More MATLAB code for 2p scope design
Posted in Software
In the last post, I mentioned how the “minification” factor (the diameter of the PMT detector divided by the diameter or…
MATLAB code for designing collection optics for 2p scopes
Posted in Software
The Tsai book chapter from Ron Frostig’s CRC book is a great resource for building your own 2p microscope. In section…
Labrigger Xmas Gift List 2010
Here’s the 2010 Labrigger Xmas Gift List.
Care to add anything?
Beam profiler
Measure the divergence of your laser beam, its stability, uniformity– all kinds of good stuff. These are useful metrics for diagnosing problems with the laser and really nailing the…
Igor Pro and Electrophysiology
Posted in Software
Igor Pro is a data analysis environment specialized for 1D time series data. It has some nice features: it handles data scaling beautifully, it has good built-in…
Software for custom 2p scopes
Posted in Software
If you build your own two photon scope, you’ll need software. I mainly use the MATLAB-based ScanImage. Vijay Iyer (Janelia Farm) has really made it a slick, stable program. It cosmetically resembles Tom…
Remote desktop software
Posted in Software
From time to time, you might catch me on my yacht, running an imaging experiment by remote desktopping into my rig from my laptop. I would use my iPhone, but I can’t fit all the windows for ScanImage onto the screen, even…
TIFFs in MATLAB
Posted in Software
MATLAB uses the open source library libtiff to write TIFF files, or they did the last time I asked. I work with multipage TIFFs a lot, and I find MATLAB is not very…
Some OSX programs & tips
This is just a quick post to highlight a few Mac OSX programs & tips that you might find useful.
Programs
Default Folder – This is how all save file dialogs should work. Watch the…
Colorblind-proof two color scheme
Posted in Software
The usual color scheme for showing co-localization is to overlay a red image and a green image and have the yellow portions show the sites of co-localization. This is problematic since red-green colorblind people…
TREES: MATLAB toolbox
Posted in Software
A new paper in PLoS Computation Biology proposes an elegant formalism for describing neuronal morphology. The reason I’m highlighting it on Labrigger is because the authors have simultaneously released a very extensive, impressive…
Processing
Posted in Software
Processing is a programming language geared towards visual artists, but it comes in handy for a lot of other purposes as well. Here are some of its finer points:
Open source
Integrated IDE (see below)
Lots…
Feeds and Forum
Recent comments
- Peter on The Art of the Cold Email in Science
- Sias Jordaan on More money than god and a death wish
- L. on Cheap DIY Kwik-Cast
- Coralie Hoffmann on Cheap DIY Kwik-Cast
- superkuh on Milk and Brain
- L. on Options for pulse compression for 2p imaging
- Peter on Options for pulse compression for 2p imaging
- L. on Options for pulse compression for 2p imaging
- B on Options for pulse compression for 2p imaging
- If you didn’t record it, it doesn’t count. – Labrigger on Writing it down
Tag cloud
3d printing analysis arduino behavior calcium imaging collaboration computing construction course data acquisition dissemination electronics electrophysiology equipment fluorescence funding gadgets imaging jobs labview laser laser cutting machining manipulators materials MATLAB meeting microscopy openness optics osx pcr processing python references robotics two-photon video visual stimuli water jet cutting- June 2024
- May 2024
- April 2024
- March 2024
- February 2024
- January 2024
- December 2023
- November 2023
- October 2023
- September 2023
- August 2023
- July 2023
- June 2023
- May 2023
- March 2023
- January 2023
- November 2022
- October 2022
- September 2022
- July 2022
- June 2022
- March 2022
- September 2021
- November 2020
- July 2020
- June 2020
- May 2020
- February 2020
- November 2019
- October 2019
- June 2019
- December 2018
- November 2018
- October 2018
- July 2018
- June 2018
- May 2018
- April 2018
- March 2018
- February 2018
- January 2018
- December 2017
- November 2017
- October 2017
- September 2017
- August 2017
- July 2017
- June 2017
- May 2017
- April 2017
- March 2017
- February 2017
- November 2016
- September 2016
- August 2016
- July 2016
- May 2016
- April 2016
- March 2016
- February 2016
- January 2016
- December 2015
- November 2015
- September 2015
- August 2015
- July 2015
- May 2015
- April 2015
- March 2015
- February 2015
- January 2015
- December 2014
- November 2014
- October 2014
- September 2014
- August 2014
- July 2014
- June 2014
- May 2014
- April 2014
- March 2014
- February 2014
- January 2014
- December 2013
- November 2013
- October 2013
- September 2013
- August 2013
- July 2013
- June 2013
- May 2013
- April 2013
- March 2013
- February 2013
- January 2013
- December 2012
- November 2012
- October 2012
- September 2012
- August 2012
- July 2012
- June 2012
- May 2012
- April 2012
- March 2012
- February 2012
- January 2012
- December 2011
- November 2011
- October 2011
- September 2011
- August 2011
- July 2011
- June 2011
- May 2011
- April 2011
- March 2011
- February 2011
- January 2011
- December 2010
- November 2010
- October 2010
- September 2010
- August 2010
- July 2010
- June 2010