Category: Software

CodeV, Zemax, OSLO, or …

Trying to decide which optical design software to use? Just try them out and decide for yourself. I like how Steve Eckhardt (great guy, btw, in case you’re looking for someone to consult with) summarized their different strengths: “CodeV’s Global Synthesis is an extremely powerful global optimizer while Zemax makes it easy to take control



PackIO for NI devices

Adam Packer wrote some LabVIEW software for acquiring and generating data from National Instruments cards called PackIO. It is meant to trigger and synchronize equipment as well as record any data, with a few specific modules for electrophysiology. The nice thing is that you can do just about everything in a hardware-timed fashion, so you’re



Voice control

Voice control has just recently become interesting to me. Ikuko bought me an Amazon Echo and I’m surprised at how useful I find it. I’m also surprised at how well it works– it can decipher my commands even when I’m whispering or mumbling from across the room. But the usefulness is what surprised me the



an hdf5/matlab file browser

Michael Graupner has coded a nice program for browsing and managing hdf5 files (closely related to MATLAB files) called hdf5Manager. And it’s open source.



New spike inference for SIMA

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 approach permits the efficient estimation of the most likely spike train underlying a sequence of calcium imaging observations. The new



RStudio – MATLAB-like IDE for R

Carson Chow recently shared his post-MATLAB suite of programming tools, and it involves RStudio, which is open-source. “I had planned to replace Matlab with Python, Julia, and R but I have found that R and Julia have been sufficient for my requirements.” It’s a nice environment and something to try if you’re looking for an



Embrio for LabVIEW like programming of Arduino hardware

Embrio isn’t completely open. They want to sell $50 licenses. Let’s get that out of the way first. However, it is an interesting alternative for programming Arduino hardware. It’s a visual programming environment, like LabVIEW. In some ways, it is richer than LabVIEW, and perhaps more comparable to MAX in that variable values can be



Remote, web-based analysis

Jeremy Freeman and his lab are developing tools for analyzing data using a workflow that is fundamentally more scalable not only in terms of computing power and data set size, but also in collaboration and sharing. The one-person, one-machine approach to data analysis can be highly efficient, but collaboration and scaling up computational power can



FocusStack and StimServer for MATLAB

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. The paper is open access. In particular, Dylan’s MATLAB functions MappedTensor and TIFFStack are worth checking out. Both provide



SIMA update – for 2p calcium imaging

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 of ROIs across different imaging sessions, signal extraction). These new versions now support 3D datasets, allowing for analysis



NES – NeuroMat – browser-based data collection

NES, from NeuroMat, is an open-source tool to manage clinical data gathered in hospitals and research institutions. Here’s their github link. More info from the lab.



Proper export for MATLAB figures

Getting nice figures out of MATLAB can be a challenge. Sometimes it’s fine, but if you’ve hit upon a figure that simply isn’t exporting nicely (bad vector rendering, lost transparency, etc.), check out the export_fig project on Undocumented MATLAB.



Time-bandwidth product

Ultrafast pulses are formed through interference of different wavelengths of light. Think of Fourier transforms, and how pulses can be generated through constructive and destructive interference of wavelengths with aligned phases. These wavelengths are close to the center wavelength, and spread over a wavelength bandwidth. Shorter pulses require wider bandwidths, and the product of pulse



Python ephys and calcium imaging analysis code

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 Ephus, but the majority of the code is acquisition platform agnostic. It’s called d_code.



Online app for comparing fluorescent proteins

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