NeuroMatic, data analysis and acquisition software

Misc ||| Home | Install | Links | Release Notes |||

Analysis ||| Basics | Data / Folders | Sets | Groups | Graphs | Main | Stats | Spike | Event | Fit | MyTab | Macros | Configs |||

Acquisition ||| Clamp | File | Notes / Log | Folders | Board | Stims | Stim Misc | Stim Time | Stim Board | Stim Pulse | Analysis | Configs |||


File Tab



Folders / Files

NeuroMatic data folders contain the acquired data, a copy of the stim folder used to acquire the data, a copy of the Notes folder, channel folders to hold the channel display global variables, and all other global variables necessary to interact with NeuroMatic, such as the Set and Group waves. These folders are by default saved automatically to your disk.

Prefix Name – during initialization, NeuroMatic will create a data folder prefix based on the current date (e.g. nm05Sep08). This is accomplished using Igor’s date() command, in which case the format of the date will depend on your operating system and your Configurations entered in the Date & Time control panel (Macintosh) or the Regional Settings control panel (Windows). In our lab we use a long date format of dd MMMM yyyy. You can change the prefix name if you prefer to use a different one.

Cell Sequence Number – cell counter that follows the prefix name (e.g. nm05Sep08c0). Once you are finished recording from a cell, click the “+” button to increment this sequence number. The folder sequence number will automatically be zeroed. If you do not wish to use the cell sequence identifier, enter NAN.

Folder Sequence Number – a three digit number combined with the folder prefix name and cell sequence number (e.g. nm05Sep08c0_002). The sequence number is automatically incremented after each recording.

Stim Suffix – a short string to identify the name of your stimulus protocol, added to the end of the stimulus folder name (e.g. nm05Sep08c0_002_vstep). Enter nothing if you wish to omit this identifier. Save your stimulus protocol to save this identifier for future use.

Save To – the external directory path where data files are to be saved. If empty, NeuroMatic will initially save with a dialogue prompt. To set the path, place cursor in box and hit return. You will be prompted to select a directory path. You can also set the path via configurations (NeuroMatic > Configs > Edit > Clamp).

Save Format – checkbox option to select the format of saving to an external data file. Igor 4 users have the option of saving as a NeuroMatic binary file and/or an Igor Experiment. Igor 5 users have the option of saving as a NeuroMatic binary file and/or as an Igor binary file (recommended).

  • Saving as a NeuroMatic binary file saves individual data folders as compact binary files with extension “nmb”. This format allows appending, which is used in the save while recording mode (see below). The draw-back of this format is that, depending on the speed of your computer, opening and saving data files CAN BE SLOW.
  • Saving as an Igor experiment file is equivalent to Igor’s “Save Experiment” file option (see Igor SaveExperiment command), in which case all data folders and variables in the current Igor experiment are saved to a data file with extension “pxp”. If you use this option, it is best to have the “close previous” data folder option selected true in order to prevent accumulation of data folders in successively recorded data files. This file type will be larger than a NeuroMatic binary file since it will contain all global variables associated with running NeuroMatic, located in the Packages folder.

  • Some users may prefer to save their data not as individual files, but as a single Igor experiment at the end of their experiment. In this case, save “never” should be selected (see below). You must then use Igor’s “Save Experiment” command to save your data at the end of your experiment. However, you may find the accumulation of data folders and therefore RAM prohibitive. Also, this method does not safe-guard against the loss of data during a computer crash.

  • Unlike an Igor Experiment, an Igor binary file includes only the current data folder that was just acquired, similar to a NeuroMatic binary file (see Igor’s SaveData command). This file format is the quickest and most efficient method of saving and opening data files. Hence, we highly recommend using NeuroMatic with Igor 5 and saving data as Igor binary files.

Save When – checkbox option to select when data files are saved (never, while recording or after recording).

  • Never – if selected, it is your responsibility to save your data as you please. The close previous data folder option will not function in this mode. Note, this option is not recommended since it does not safe-guard against the loss of data during a computer crash.

  • While Recording – if selected, data will be saved as a NeuroMatic binary file. Waves will be appended to the external data file once they are acquired. This option safe-guards against a computer crash during acquisition. For Igor 4 users, it is also the quickest way to save data files. However, depending on the speed of your computer and the rate of acquisition set by your stimulus protocol (i.e. the wave and repetition interlude times), Save While Recording may effect the rate of acquisition, and therefore should be used with caution.

  • After Recording – if selected, data will be saved after all sweeps have been acquired after selecting Record. This method may be slow for NeuroMatic binary files, depending on the speed of your computer. It is the only option available for Igor experiment and Igor binary files.

Close Previous Data Folder – checkbox option to close the previous data folder after NeuroMatic creates a new one for recording (default). This prevents accumulation of data folders during your experiment, and allows maximum RAM for Igor.


Notes

You can enter values for your name and experiment title on the configuration tab, or you can select Edit and enter values, or create new note variables, via the Notes Table.

Log

After each recording, Notes are saved to a Log Folder. This folder will automatically be saved to an external binary file if auto save is checked true. While you are acquiring data, the log can be displayed as a table or a notebook or both.


Misc ||| Home | Install | Links | Release Notes |||

Analysis ||| Basics | Data / Folders | Sets | Groups | Graphs | Main | Stats | Spike | Event | Fit | MyTab | Macros | Configs |||

Acquisition ||| Clamp | File | Notes / Log | Folders | Board | Stims | Stim Misc | Stim Time | Stim Board | Stim Pulse | Analysis | Configs |||


Please send feedback about NeuroMatic to Jason@ThinkRandom.com

Copyright © 2002-2009 ThinkRandom.com. All Rights Reserved.