Following up SIMA, which has been covered here before:
The SIMA team has released a new version of its toolbox that includes a spike inference algorithm developed by Eftychios Pnevmatikakis and Liam Paninski’s group. This…
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…
Andrew Giessel wrote some analysis code in Python when he worked in the Datta lab. He has since moved on to another venture, but he open-sourced the code. There are import routines for data from ScanImage and…
Olympus released a suite of new objectives this year, and one of them is this 10x/0.6 NA. This is probably the longest focal length (180/10 = 18 mm) objective you can get and use with a…
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…
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…
If you like Labrigger, you should register for this Short Course at the SfN meeting.
Short Course #1: Advances in Multineuronal Monitoring of Brain Activity
Spencer Smith will be talking about the work SLAB…
There are a bunch of GCaMP6 mouse lines out now, from Hongkui Zeng (Ai93, Ai95, Ai96 are available), Cris Niell, GENIE (paper), and others. Have you tried any of these? Labrigger…
Sign up now for SfN Short Courses. In addition to the excellent material that is covered, these workshops can be a great opporunity to make new connections with like-minded people– scientists with the similar interests,…
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…
Thorlabs released a ridiculously sized (264 MB) PDF catalog for their life sciences imaging. Despite the size, I recommend downloading it and checking it out. There are several items and lots of product details that are…
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…
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…
