Tag: fluorescence

Tons of 2p spectra – twophotondyes.com

  Daniel Fiole is curating a nice resource for 2p cross sections: twophotondyes.com There’s a lot here. It’s not just dyes, he has links for fluorescent proteins as well, and there’s 3p data linked to as well: Prior posts on 2p cross sections:  



CANDLE-J for denoising 2p data

Collaborative Approach for eNhanced Denoising under Low-light Excitation, or CANDLE, is a denoising algorithm specialized for the type of images that are acquired in 2-photon imaging applications. There’s code for both ImageJ and MATLAB available at that link. Here’s a write up on it. The raw images are on the left, and the denoised (via



Online app for comparing fluorescent proteins

George McNamara recently posted a comment on spectra, which referenced this online app which is handy.



ImageSurfer 64-bit

UNC-Chapel Hill’s Computer Integrated Systems for Microscopy and Manipulation team released a new version of their popular ImageSurfer software. All 64-bit, with versions for Linux, OSX, and Windows.



What’s your favorite LUT?

Parula is the new default colormap for MATLAB (namesake above, actual map below). It probably collapses to grey better than jet (which is good for colorblind readers). You aficionados care dearly about LUTs, as does Labrigger. Share your preferences in the comments. Do you prefer MATLAB’s jet colormap? ImageJ’s “Hot” LUTs (e.g., Green Hot, Cyan



SIMA – Image analysis from the Losonczy lab

(This post by the SIMA Team.) The SIMA (Sequential IMage Analysis) package facilitates analysis of time-series imaging data arising from fluorescence microscopy. The functionality of this package includes: – correction of motion artifacts – segmentation of imaging fields into regions of interest (ROIs) – extraction of dynamic signals from ROIs The included ROI Buddy software



The commoditization of image sensors

About 25 years ago, pro-level audio recording technology was prohibitively expensive for home studios. Then, digital audio technology like the Alesis ADAT enabled working class musicians to produce high fidelity recordings. The fast development of audio recording technology has pushed prices down and performance up to a point where 24-bit/192kHz digitizer kits are cheap, and



Optomechanics and microscopy technical notes – many items

Vojnovic’s group at Oxford has dozens of technical notes. Most are concise, and include software code, if applicable. SolidWorks files and PCB files are available on request. Here are a few examples: A motorized 4-way optical path selector Run by a servo, < 100 microrads reproducibility A power supply for a tunable lens Devices like



SciScan: Scientifica’s two photon software

My friend Bruno has written some very nice software for Scientifica’s two photon microscope systems. It’s called SciScan. It’s written in LabVIEW and runs both their conventional galvo and resonant systems. These screenshots are all from the conventional galvo version of the software, but the resonant version looks almost identical (there’s no arbitrary line scan



Two photon technical notes

Here’s a collection of Labrigger posts, technical notes and whatnot, on 2-photon imaging. 2010 – Building a 2-photon microscope 2011 – Building a 2-photon microscope, 2011 edition 2010 – PMTs for 2-photon imaging 2011 – Photon counting and Hybrid PMTs 2011 – More on photon counting 2010 – Lasers for 2-photon imaging More on two-photon



Fast resonant scanning two-photon scope from UCLA

Here’s an update on the scope from Joshua Trachtenberg’s team. If you want one, contact them at: info.neurolabware@gmail.com This is another moving objective microscope, like the Sutter (Denk/MOM) scope, and the Thorlabs scope. Here’s a couple shots of objective rotation: Although it’s not shown in these images, the objective can be configured to move in



Scattering in tissue

Post by Jeffrey Stirman The opacity of the brain is one barrier to optically imaging individual neurons and their connections. Scattering in tissue is the main reason tissue is not transparent; absorption also plays a role but much less so. Perfusing tissue with a substance to match the index of refraction throughout the preparation (and



Variability where you really don’t want it

Post by Christian Wilms I’ll admit it: I’m lazy. When I use a calcium indicator and need to know its physico-chemical properties, I like to simply look it up in the manufacturer’s catalogue or website. Of course I don’t expect those values to be perfect, but close enough for most purposes. Turns out that isn’t



Photoswitchable GECI

Many red fluorescent proteins go through a green fluorescent stage prior to becoming fully folded into their mature red fluorescent state. In fact, some proteins can be photoswitched in and/or out of their mature red state, e.g., Dendra2, EosFP, and Kaede. Given this protein engineering know-how, perhaps it was just a matter of time before



Interview with the developers of HelioScan

Last Monday, Labrigger covered HelioScan, a LabVIEW-based, two-photon laser scanning microscopy software suite. Marcel van ‘t Hoff (left) and Dominik Langer (right) are the two main developers of HelioScan. They were kind enough to answer some interview questions for Labrigger. LR: Are there special considerations you had to make when designing HelioScan? What measures did