GEBA - Project

Getting Started:

Launch BatchTINTV3. Once you launch the GUI you should see a window with the title "BatchTINT - Main Window", pictured below.
Choose a directory. Near the upper left portion of the Main Window lives a "Choose Directory" button. Adjacent to this button is a text field that states the directory that will be analyzed by this GUI. If this is the first time you have launched BatchTINTV3 you will likely see text in this field that states something to the effect of "Choose a Directory!", otherwise it will likely be the last analyzed directory. If the directory in this field is not the one you wish to analyze, press the "Choose Directory" button. Note: If you do not want to go through the directory selection dialogues, feel free to just copy and paste the file-path of your directory of interest into the text-filed adjacent to the "Choose Directory" button.
- Upon pressing the "Choose Directory" button you will see a bunch of boring text that states what type of directory you should choose (pictured below). Again there is a "Choose Directory" button. Press this button to launch a file picking window. This whole thing could probably be simplified to just having the first "Choose Directory" button launch this window instead.
- Now you can finally choose the appropriate directory. BatchTINTV3 can operate in a "batch" and "non-batch" mode. Below is an example of both the modes. In the examples the files with the asterisks (*) are the ones that will be analyzed by the GUI. The default is the "batch" mode which will analyze all the sessions that are contained within the sub-directories of a chosen directory. However, in non-batch mode, it will analyze the files held directly within the chosen directory without iterating through any sub-directories.
  - Batch Mode Example:
```
/Chosen_Directory
    /SubDirectory1
        *SD1_Session1Files
        *SD1_Session2Files
    /SubDirectory2
        *SD2_Session3Files
        *SD2_Session4Files
    /SubDirectory3
        *SD3_Session1Files
    ChosenDirectory_Session5Files
```
  - Non-Batch Mode Example:
```
/Chosen_Directory
    /SubDirectory1
        SD1_Session1Files
        SD1_Session2Files
    /SubDirectory2
        SD2_Session3Files
        SD2_Session4Files
    /SubDirectory3
        SD3_Session1Files
    *ChosenDirectory_Session5Files
```
- Click on Apply. Once you have finished choosing an appropriate directory, you have to press the "Apply" button to officially make these changes. If you leave the checkbox, it will also save this directory in a .json file and the text-field will be set to the chosen directory for next time the GUI is launched.
- The Queue below should populate with the session filenames of unsorted files belonging to the chosen directory (pictured below). If there are no files, the directory is invalid, all the files within the directory with the chosen mode are already analyzed, or there are no sessions within the chosen directory to begin with.
Double check the analysis mode. As mentioned earlier there are two modes: batch and non-batch. If you want to run in batch, ensure that the "Non-Batch?" checkbox below the directory text-field is unchecked (this is true by default). Alternatively, you can check this box if you want to run in the non-batch mode.
Check the "Run Silently" checkbox if you want to run in the "silent" mode. When Axona implemented the command prompt interface with Tint, it also added a "silent mode". This mode will essentially launch the KlustaKwik window, but will immediately minimize it. It can be annoying as it is not entirely run in the background, however this is the best option that exists so far. If you do not "run silently" all the sorting windows from KlustaKwik will be launched and kept open. You the non-silenced mode as as it will provide a visual cue as to when the sorting has finished.
Determine how many tetrodes you want to concurrently analyze. To the right of the "Run Silently" checkbox is a "Simultaneous Tetrodes" text-field. The value in this filed will determine how many concurrent tetrodes you want to analyze. For example, if the value was set to two, then two KlustaKwik windows would be opened analyzing the first two tetrodes (.1 and .2) at the same time. After sorting the first two tetrodes has completed, the next two tetrodes will begin (.3 and .4), and so on. Note: it will wait for the first batch of concurrent tetrodes to be completed before moving onto the next. For example, if .1 finishes before .2, it won't launch .3 (to replace .1) until until .2 has also finished.
Append Cut (optional, likely unnecessary): this is a string (text) value that will be appended to the .cut filename to avoid overwriting existing .cut files. Traditionally if you are analyzing the following tetrode file: C:/example_directory/example_session.1 (session basename followed by extension denoting the tetrode number), then the .cut file that would result from this tetrode would be named the following: C:/example_directory/example_session_1.cut (session basename, with a '_tetrode#.cut' appended). If you include an Append Cut value, the new filename would be the following: C:/example_directory/example_session[AppendCutValue]_1.cut, where [AppendCutValue] is replaced by whatever you have placed within the Append Cut text-field. My purpose for adding this functionality was because I was testing other spike sorting methods (i.e. MountainSort), and wanted to keep multiple .cut files belonging to the various methods.
Confirm that the Klusta Settings are correct. At the bottom of the Main Window is a row of buttons, one of the buttons being "Klusta Settings". If you press this aforementioned button it will bring up a window with familiar options (Pictured Below). These options are in the same layout as the KlustaKwik interface window within Tint. Change these as you please and press "Apply"
1. Basic Settings: These will include many familiar parameters pictured below.
  - Channels to Include: maybe you do not want to included all the recorded channels (Tint uses the Tetrode format, so there are only channels 1-4 listed), here is where you can discard channels.
  - Clustering Features: these features will be used to sort the data within KlustaKwik. The defaults are the following: PC1, PC2, PC3, and PC4. I do hear that some labs include energy (En) within the included features, however I have not played around with these too much.
    - A: amplitude of spike
    - Vt: voltage at "best time" on each channel, essentially the time value that represents the maximum variance in the spike values.
    - P: peak value
    - T: trough value
    - tP: time of peak
    - tT: time of trough
    - En: energy of spike
    - Ar: area of spike
  - Reporting Options: these options impact the messages provided by KlustaKwik/Tint.
    - Verbose: when checked, the messages from KlustaKwik are more detailed.
    - Screen: when checked, the progress messages from KlustaKwik will appear in the Command Prompt.
    - Log: when checked, it will produce a .klg.N log file from KlustaKwik.
  - Miscellaneous Settings: these settings are specifically for BatchTINTV3 and are likely new to you.
    - Delete Temporary Files: much of the files produced from KlustaKwik you will not need. Therefore when checked, these files will be deleted after the .cut files have been created.
    - Move Processed Files: after the files have been processed, they will be moved to a "Processed" folder if this option remains checked.
2. Advanced Settings: these are advanced settings that are used for KlustaKwik, they should be familiar to you if you have used Tint.
3. Feel free to press the "Default" button if you are have changed things by accident and want to revert back Tint's default settings.
Run! You can now press the "Run" button in the Main Window and analyze all the files listed in the Queue. If you add more files to the chosen directory (keeping in mind the mode that is selected), these sessions should be added to the queue if they are not already sorted.

BatchTINTV3 User Guide Draft

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