Tag: dissemination

Actually useful comments on scientific blogging

I came across Rachel Thomas’ comments on blogging in the context of machine learning, and they’re good. I’ve been telling people things like this for awhile now and Rachel distills them better than I do. I’ll quote some of my favorites, but check out her post to read the full story. This single point was

Pre-preprint: blogging a project

SLAB is trying something new with one project in the lab. Prior to drafting a preprint, we’re blogging the project and sharing the results and analysis. We invite anyone to comment on the work.

New category of posts: papers

In the past, Labrigger has only rarely posted about relevant papers. That ends today. Now there’s a new post category for papers, and it’ll be used to highlight publications that are of potential interest to you, the community.

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.

Colorbrewer for color schemes

Colorbrewer was designed for cartography, but is useful for figure color schemes and look up tables (LUTs). The web interface is slick, offers an immediate preview, and the look up table can be exported. Colorblind-safe and print-safe options can be designed. via Previously

Field of view = 3.5 mm with cellular resolution

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 an air immersion objective with about a 9.5 mm working distance. Rapid dissemination is a priority. If you’re interested, contact

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

Reminder: SfN Short Course

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 has been doing designing and building custom optical systems for wide field of view two-photon imaging. These recent comments provide a

Cubehelix color scheme

Cubehelix is a color scheme that retains contrast as it is desaturated (top), as opposed to a more typical rainbow scheme (bottom). It’s great for look-up-tables (LUTs). Dave Green’s web site has multiple implementations of the color scheme, including code for R and MATLAB. More… Colorblind-proof color schemes Daltonization By the way, the If We

Pitch in and share!

Don’t be shy. If you have a tip to share, however small or big, please do so using the new link above. You can do it anonymously, if you like. Or you can get full credit. Or initials, or a pseudonym. Whatever you want. And it can be as brief as you like. Simply a

PubPeer browser plugins for PubMed

PubPeer has released browser plugins that add a line to PubMed results if there are comments on PubPeer for those publications. It looks like the example above. The install took less than 10 seconds. More on PubPeer

Preserve your rights – Scholar’s Copyright Addendum Engine

Creative Commons‘ science section has an easy-to-use web page that generates a PDF form you can attach to the publisher’s copyright form to ensure you reserve certain rights. More info from Cornell Previously on Labrigger: DIY open access Future publishing Hat tip to LC

Design tips for data tables

Most scientists have adopted minimalistic design principles for graphs. We still sometimes see 3D bar charts, but it’s rare. Data tables are another story. Sometimes journals take the formatting of data tables out of the hands of the authors. Perhaps they recognize that it’s an under-appreciated art. The default tables that come out of some

Protocols.io – 3 days left

As Labrigger mentioned earlier this week, ZappyLab is running a Kickstarter campaign to jump start their crowd-sourced protocol repository, Protocols.io. Perhaps the most attractive reward they’re offering for pledging are the Black Russian Espresso cookies, made with vodka and Kahlua. The idea of Protocols.io is to mitigate the tendency for every lab to reinvent the

PLoS One requires full data release with publication

authors must make all data publicly available, without restriction, immediately upon publication of the article Examples could include spreadsheets of original measurements (of cells, of fluorescent intensity, of respiratory volume), large datasets such as next-generation sequence reads, verbatim responses from qualitative studies, software code, or even image files used to create figures. Data should be