In msuefishlab/tdmsviewer: View TDMS files as a RShiny app

TDMSViewer User Manual

Source Code

https://github.com/msuefishlab/tdmsviewer

Installation

TDMS Viewer is designed as an R package, to be installed using a package manager. In our case, we install it from github. Open RStudio and run

install.packages('devtools')
library(devtools)
install_github('msuefishlab/tdmsviewer')

After running this it should install the tdmsviewer app and its dependencies automatically. Windows users please note that some additional dependencies need to be installed manually.

To make sure you are installing the version mentioned in this guide, you can also run

install_github('msuefishlab/tdmsviewer@0.8.0')

But you might benefit from using the latest version

Windows specific installation errors

The install_github function doesn’t work fully properly on Windows On Windows, the install_github function it fails to install some dependencies, so you may have to install them manually.

Possible dependencies you have to manually install includes

install.packages(c('htmlwidgets','DT','RSQLite','Rcpp', 'ggplot2'))

Note that this is only a problem on windows, other platforms should install all dependencies automatically when you use install_github('msuefishlab/tdmsviewer')

Using TDMSViewer

Once the library is installed, you can then use it by running

library(tdmsviewer)
tdmsviewer()

This will launch a browser that you can then use to open your files and navigate the webapp

Note that you may also want to set the "base directory" of the app to either broaden or limit the subfolders that the webapp can access. Simply run instead

library(tdmsviewer)
tdmsviewer(basedir="C:\\")

To run from root C: drive on windows. Or

library(tdmsviewer)
tdmsviewer(basedir="C:\\Users\\YourName\\Desktop\\FolderWithTDMS")

By default the basedir is your home directory when using Linux/MacOS or the My Documents folder when using Windows

Selecting TDMS files

The first thing to do to select TDMS files is to click the "Choose TDMS file" button. This will launch a file selector, and you will open a specific directory that contains TDMS files.

Figure 1. "Choose TDMS file" button

Figure 2. The "Choose TDMS file" file selector

Figure 3. After selecting a file, it is automatically plotted over the range [0-1] seconds and metadata is displayed

TDMS metadata

• The "TDMS properties" contains file-level metadata e.g. gain, pH, time/date, name, etc.

• The "TDMS channel properties" contains channel-level metadata e.g. sample rate

Most of the files we look at only have one channel, but the "object" selector lets you see a list of available channels

Navigating TDMS files

Once the chart is plotted on the screen, there will be several options

1) Range: this is the start and stop time to be plotted from the TDMS file

2) Zoom in (+) narrows the start and stop range

3) Zoom out (-) widens the start and stop range (doesn’t go past 0 or end of file)

4) Move left (<) shifts view to the left

5) Move right (>) shifts view to the right

You can also click and drag your mouse over the plot itself which automatically zooms in on a specific area

Saving EODs

You can use the "Save EODs in current view" button which will automatically run a peak finder over the range from start to end.

This peak finder finds data points where the data in this range is$\text{\ mean}\left( x \right) \pm n*stddev(x)$ where n is user configurable setting for threshold.

This captures "positive" of "negative" peaks, and after the peak finder is fixed. The app will output a text that says "Saved N peaks, (x+, y-)" when complete (Figure 4)

Figure 4. Selecting the "Save EODs in current view" captures EOD peaks using either the sigma or voltage threshold. A progress bar is displayed and a text is outputted about the saved peaks

Saved EODs

After the EODs are saved using the peak finder, they will be saved to a SQLite database (which is persistent across sessions) and you will see a list of EODs on a table

Figure 5. The "Saved EODs" tab shows a list of EOD that were captured by peak finding, and can display the EODs overlaid on each other

Figure 6. After clicking "Select all" it will plot all waveforms on a single plot

The following transformations are supported

1) Normalize selected EOD(s) - clip the maximum to minimum value 0-1

2) Pre-baseline subtract – subtract mean of 100 samples before normalization

3) Post-baseline subtract – subtract mean of 100 samples after normalization

4) Average selected EOD(s) – collapse all EODs into average waveform

Downloading data from Saved EODs page

The app supports downloading the EOD data from the "Saved EODs" page with two buttons

• "Download waveform matrix" gets a CSV where columns are volts, rows are timepoints

• "Download average waveform" gets a CSV with one column (volts), rows are timepoints

Important tip about the Saved EOD page:

You can also use the "search" function to the right of the table to filter the EODs that you are interested in, and it will only plot the EODs that match the "search" that you submitted

For example, you can search part of the filename that you saved the EODs from or similar

Finding landmarks on the "Saved EODs" tab

To identify landmarks, you can click the "Find landmarks" button which will automatically identify the main landmarks

Figure 7. Plot of average waveform before identifying waveforms

Figure 8. Waveform after clicking "Find landmarks" button

Figure 9. Giving a name for your landmarks which is used on the "Landmarks" tab

Evaluating landmarks in the "Landmarks" tab

The "Landmarks" tab of the application allows you to view data about the annotated landmarks for a given set of waveforms.

To get started, first download a set of EODs using the "Download waveform matrix" in the "Saved EODs" tab, and upload it to the "Landmark" tab for evaluation.

Then you can choose the set of landmarks (e.g. you might have a set of landmarks for larval recordings, adult recordings, etc). The result will be a plot of the voltage values at that particular location, and a textual output of the mean and stddev of the voltage values

Figure 10. Overview of the "Landmark" plots the voltage value for multiple EOD waveforms at the annotated points that are given

Conclusion

The TDMS Viewer offers a streamlined approach to analyzing EOD data. You can interactively analyze and collect EOD waveforms from different TDMS files using the application, and the results will be saved into a local "database" that you can access at a later time. You can also create custom plots of the waveforms, download waveforms, annotate the waveforms with landmarks, and get statistics.

msuefishlab/tdmsviewer documentation built on May 23, 2019, 8:17 a.m.