analysis:nsb2015:week3long
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analysis:nsb2015:week3long [2015/07/16 17:37] mvdm created |
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| ~~DISCUSSION~~ | ~~DISCUSSION~~ | ||
| - | ===== Module 5: Visualizing neural data in MATLAB ===== | + | ===== Module 3: Visualizing neural data in MATLAB (long version) ===== |
| Goals: | Goals: | ||
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| First, make sure you have the folder ''R042-2013-08-18'' from the data share, and that this is placed in a sensible location (NOT in a %%GitHub%% or project folder!). | First, make sure you have the folder ''R042-2013-08-18'' from the data share, and that this is placed in a sensible location (NOT in a %%GitHub%% or project folder!). | ||
| - | This data set was collected from the dorsal CA1 region of the hippocampus of a rat performing a T-maze task, using a drive with 16 independently movable tetrodes. Spike and LFP data was recorded from each tetrode; possible spike events were detected online and stored for offline spike-sorting, and LFPs were sampled at 2kHz and bandpass filtered between 1-475Hz. (A quirk of this particular data set is that certain time intervals are cut out of the spike data, but not the LFP. So you may notice some odd looking gaps in the rasterplot later.) | + | This data set was collected from the dorsal CA1 region of the hippocampus of a rat performing a T-maze task, using a drive with 16 independently movable tetrodes (by [[https://github.com/aacarey|Alyssa Carey]] for her Master's thesis work). Spike and LFP data was recorded from each tetrode; possible spike events were detected online and stored for offline spike-sorting, and LFPs were sampled at 2kHz and bandpass filtered between 1-475Hz. (A quirk of this particular data set is that certain time intervals are cut out of the spike data, but not the LFP. So you may notice some odd looking gaps in the rasterplot later.) |
| As in previous modules, use the shortcut button created in the previous module to set your path. In your project folder, create a folder with today's date and ''cd'' to it. This will be your "scratch" working directory with stuff that you don't necessarily intend to push to %%GitHub%%. | As in previous modules, use the shortcut button created in the previous module to set your path. In your project folder, create a folder with today's date and ''cd'' to it. This will be your "scratch" working directory with stuff that you don't necessarily intend to push to %%GitHub%%. | ||
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| %% cd to data folder -- replace this with yours | %% cd to data folder -- replace this with yours | ||
| fd = 'D:\data\DataAnalysisTutorial\R042-2013-08-18'; | fd = 'D:\data\DataAnalysisTutorial\R042-2013-08-18'; | ||
| - | cd(fc); | + | cd(fd); |
| %% load the data (note, may need to unzip position data first) | %% load the data (note, may need to unzip position data first) | ||
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| Finally, for data exploration it is helpful to be able to skip through the data with the arrow keys; set it up so that the left and right arrows can be used to scroll left and right. For extra awesomeness, add zoom functionality that scales the LFPs when pressing the up and down arrows. | Finally, for data exploration it is helpful to be able to skip through the data with the arrow keys; set it up so that the left and right arrows can be used to scroll left and right. For extra awesomeness, add zoom functionality that scales the LFPs when pressing the up and down arrows. | ||
| - | ☛ When you are satisfied with your work, save a copy in your project folder and push it to GitHub. Verify that your version is visible from the web. | + | ☛ When you are satisfied with your work, you can compare your implementation to the one by [[https://github.com/aacarey|Alyssa]] and [[https://github.com/youkitan|Youki]], called ''MultiRaster()''. |
| === Hints === | === Hints === | ||
analysis/nsb2015/week3long.1437082640.txt.gz · Last modified: 2018/07/07 10:19 (external edit)
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