Basic Usage walkthrough
For each experiment you want to analyze as a whole, put all .abf/.smr files in one folder. Crabsort will produce an error if you have files with different numbers or names of channels. So, if you changed the protocol halfway through, put those files in another folder to analyze separately. If you’re not sure if all your ABF files are in the same format, run crabsort.convert2crabFormat in the directory. This will convert all ABF files into MATLAB-compatible .crab files (these are simply .mat files) and will also “harmonize” all files by making sure you have the same # of channels, etc.
In the MATLAB command window, type crabsort – this will open the program.
Click on "select data file" and load the first .abf file you want to work on. I usually start with some file in the middle of a baseline recording. Crabsort will now check that all the .abf/.smr files in your folder are compatible.
Once you load thee file, you should get a window that looks similar to this. Hide any channels you don't want to look at or analyze spikes for. You can show hidden channels again by checking the channel under the "channels" dropdown menu
On the top left of each channel, if you hover over the area there are a bunch of options. The zoom options are most commonly used. Click on either the + or - to change the x-scale. (whenever you change the scale, you need to click on the magnifying glass again (so it’s not blue anymore) before you can do anything else) Change your x-scale so you can see a few cycles, or enough to get an idea of whether you are capturing all the spikes you want to ID. You can also click on the top menu “view” bar and select “full trace” to see the whole file.
Now label the channels. For example, this is an lvn.
Once you label the channel, and sort spikes for that channel, this is permanent and labels it for all files in the folder. If you make a mistake, go to the folder containing spikes (see below for where it is) and delete the crabsort.common file, then start again. Because this can mess everything up, it’s usually best to label all the channels right away, so you don’t need to go back later
- If you need to, you can customize channel names and the cells on different nerves in the preference file. Type “edit pref” into MATLAB to check out the things you can change. If you make edits, go to crabsort>tools>reload Preferences to load the new prefs.