Monthly archives: February, 2012

Feb292012February 29, 2012February 29, 20121Commentby L.

Tsien’s VoltageFluors

Posted in Tips

Roger Tsien’s lab recently published the new generation voltage sensitive dye they were presenting at SfN: VoltageFluors. As often when then Tsien Lab takes on a new field, they start by taking a completely…

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Feb272012February 27, 2012February 28, 20120Commentby L.

Nature article on releasing source code

Posted in Software

Nature just published a 4-page perspective article on the important of releasing the source code for programs used in scientific research. The authors emphasize the importance of reproducibility for results that depend…

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Feb172012February 17, 2012February 16, 20121Commentby L.

Fast z-galvo for 3D two-photon imaging

Posted in Hardware

Perhaps you’re familiar with the various AOD and piezo-based methods for two-photon imaging in 3D quickly. Here’s another way (Botcherby et al. 2012, PNAS, open access)

The used all galvos, rather than AODs or…

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Feb162012February 16, 2012February 19, 201210Commentsby L.

Intrinsic imaging on the cheap

Posted in Hardware

Intrinsic signal optical imaging is a functional imaging modality where the reflectance of red light indicates active portions of cortex. It is used for many applications, including imaging individual barrels in rodent somatosensory cortex, maps in visual cortex, and the tonotopic organization in auditory cortex.

Here is a prior Labrigger post with tips for intrinsic…

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Feb152012February 15, 2012February 15, 20121Commentby L.

Clearing tissue for imaging: index matching is not new

Posted in Hardware

The main factor that limits how deep we can image into tissue is the scattering of light. Multiphoton imaging partially mitigates the problem by using infrared light, which scatter less, and by using an excitation…

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Feb092012February 9, 2012February 9, 20120Commentby L.

The Elsevier Boycott and the Research Works Act

Posted in Uncategorized

Perhaps you’ve heard about the Elsevier Boycott aka the Cost of Knowledge. I’m not going to rehash the problem we all know so well. But here are a few links I wanted to share….

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Feb082012February 8, 2012February 4, 20120Commentby L.

Predatory open science funding

Posted in Uncategorized

There are some open access journals that seem to have relativley loose editorial standards. And by “editorial” I mean “ethical”, and by “relatively loose”, I mean “no”. These publishers have been called “predatory” open…

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Feb072012February 7, 2012February 4, 20120Commentby L.

Open Microscopy Environment, for managing microscope images

Posted in Software

The Open Microscopy Environment (OME) is a group of programmers, from academia and industry, who put together open source software packages for managing microscopy data. The emphasis is on handing multiple image formats, organizing…

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Feb062012February 6, 2012February 4, 20120Commentby L.

OpenElectrophy – for multielectrode recordings

Posted in Software

OpenElectrophy is a somewhat mature, actively developed, open source program for analyzing data from multielectrode recordings. It makes heavy use of Python and SQL and is developed by a team of French researchers including…

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Feb052012February 5, 2012February 4, 20120Commentby L.

3D Sketch-up models for Newport parts

Posted in Hardware, Software, Tips

Thorlabs and Newport have offered 3D models of their products for a long time. However, they’re typically in formats for expensive programs like SolidWorks and AutoCAD. In the past year or two, Newport has been slowly adding to their library of Google SketchUp models.

…

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Feb042012February 4, 2012February 4, 20120Commentby L.

Competition

Posted in Software, Tips

Like many of you, I went to monster truck show last weekend.

The competition reminded me MATLAB’s new thing: Cody.

It’s a bunch of problems posed as MATLAB coding tasks. For example:

Find the mean of…

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