I tweeted about this last fall. This is the best algorithm I’ve seen for segmenting and extracting time course from calcium imaging data. Eftychios Pnevmatikakis developed the code in Liam Paninski’s lab. The work…
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…
Compared to visible (vis) light, near infrared (NIR) wavelength scatters less and is less absorbed in brain tissue. If your fluorescent target absorbs vis light, then one way to use NIR is to flood the area with…
The Max Planck Florida Institute for Neuroscience is holding an imaging course Jan 11-20, 2016.
They have a really excellent line up of lecturers. A range of topics will be covered: two-photon imaging, FLIM, FRET, endoscopy, uncaging, optogenetics, SPIM, image analysis, instrumentation (alignment, system design), …
Applications are due in a few days, Nov….
Dylan Muir and Bjorn Kampa created some MATLAB code for two-photon calcium imaging experiments. First up is FocusStack, which provides a suite of analysis tools. Next up is StimServer, which coordinates visual stimulus generation and presentation. …
SIMA has recently been updated (here’s the original Labrigger post):
From the SIMA team:
We have recently released updated versions of the SIMA & ROI Buddy tools for analysis of calcium imaging data (motion correction, segmentation, registration…
In this preprint, Stirman et al. report achieving a 3.5 mm field of view with 2-photon excitation with cellular resolution. The design involves custom scan optics and a custom objective built in the SLAB. It’s…
This open source two-photon microscope system is adaptable for both slice (with substage detection) and in vivo experiments, and is built with largely COTS parts. The paper is a very nice resource.
See also, designs…
ScanImage 5 supports resonant scanning with a wide range of hardware. So custom rigs can add resonant scanning pretty easily, while sticking with ScanImage for acquisition.
(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…
Adrian Negrean, in Huibert Mansvelder’s lab, has been designing and building custom scan optics for two-photon imaging and earlier this year published his work (paper). Labrigger wants to emphasize how nice this paper is. It’s an…
Dario Ringach has written some nice software for the Trachtenberg scope mentioned before on Labrigger. They also have put together their own Cypress PSoC-based hardware box to control several parts of the system.
He set up…
Luke Campagnola, Megan Kratz, and Paul Manis recently published their in-house software for neurophysiology experiments. It’s an extensive set of tools, including multiphoton imaging, photostimulation mapping, image mosaic construction, electrophysiology, and more.
Website: acq4.org
…
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…
