Getting started with staging

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[-] Korey Kam +0 points · about 3 years ago

Hi all,

I'm a new visitor to the National Sleep Research Resource and wanted to say that the site is fantastically intuitive particularly for a student such as myself!

I am interested in performing manual and then automated sleep staging. I have successfully viewed a test edf file in the SignalRasterView app and then did the same in EDFViewer. Now, I would like to implement staging on test edfs.

Is there a matlab tool you recommend for both manual and automated staging/event stamping (with requisite xml annotation compatibility)? I'd be particularly interested in a tool that has built in functions for assessing sleep measurables. Furthermore it would be great if the tool had signal processing capabilities to assess staged epochs (without me needing to modify data struc in order to run matlab sigprocfunctions).

As a new user I greatly appreciate the emphasis placed on ease of use. Thanks, Korey

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[-] remomueller +0 points · about 3 years ago

Hi Korey and welcome to the site! I'm going to forward this to our resident sleep tools expert, Dennis Dean, and hopefully he can get you started in the right direction.

Also, we do have staging files in a fairly simple format for the SHHS dataset. Here's a README.txt to get you started, and you can find the staging files here: https://sleepdata.org/datasets/shhs/files/annotations-staging

Michael Rueschman will also be preparing staging files for the CHAT dataset soon, so keep an eye out for those. Thanks!

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[-] DennisDean +0 points · about 3 years ago

Hi Korey,

Welcome to the site. It is very exciting to feel your enthusiasm. I will break down your questions into discrete steps. I would recommend approaching staging systematically. I believe that you could proceed in a way that you can develop some nice tools while generating important research findings.

Sleep Staging Papers. I would recommend that you start by reviewing Gross et al. and Leclercq et al.. I have always wanted to go through the Gross paper in detail. Please respond with your thoughts.

Please let us know how you intend to proceed.

SignalRasterView was developed specifically to view signals and annotations. There are a lot of possibilities. Our plan was always to convert the GUI from generating a figure to writing to a figure in a GUI. With just a few buttons, it would be straight forward to scroll through the signal and see the data.

(1) SignalRasterView and Sleep Stages. I would recommend adding the annotation file as an input. If the input is present, sleep stage information would be added to the signal raster view. I would recommend changing the background color of each epoch by stage.

(2) SignalRasterView and Scoring. Our scorers tell us that they want to look at the data at multiple scales and include other signals. Consider adding a second figure panel. A revised GUI could be added as a 'scoring' configuration option.

I wrote SignalRasterView, so feel free to discuss strategies for adding sleep stage scoring. It may be possible to coordinate effort.

Good Luck!

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[-] Korey Kam +0 points · about 3 years ago

Thank you all for the insight!

I see great utility in the Gross 2009 paper and have contacted the senior author for a usable version of the matlab code (both manual Sleep-Scorer and the Auto-Scorer). If I get a reply and a link, I'll test it out using some of the prestaged edfs/xmls. I have seen some patent hits on this software with those authors so it may not be freely available for research.

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[-] DennisDean +0 points · about 3 years ago

The software described in Gross et al. can be found online and is freely available. You can download the software here: https://secure.nouvant.com/umich/technology/4582/license/142.

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