ToF-AMS Analysis Software

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ToF-AMS Analysis Software Wiki

All the text from BEGIN to END will be removed by the 2009 User's meeting.

BEGIN

A copy of the pdf sent to Pika 1.06J beta testers can be downloaded here

Pika 1.06J beta testers:

  • Upgrade to Igor 6.11

To use a new Pika template:

  • Download new .pxt at here


To upgrade an existing experiment:

  • Upgrade Squirrel ipfs to 1.47H. Download zipped file of ipfs at here.
  • Upgrade Pika ipfs to 1.06J. Note that there are two new ipfsin 1.06J: PK_frag_xx and Pk_elemAnal_xx. There is now a total of 7 PK_yy_xx_ipfs. Download zipped file of ipfs at here.
  • Create a data folder called HR_frag and load all waves from the file HR_fragWaves_1_06J.itx into it. Download zipped itx file at here.
  • Kill and recreate the main Squirrel panel and the main Pika panel.

(After this step it would be a good idea to save your experiment as version 1_06J or something else).

  • Play!


Initial comments From Doug, Manjula, Jose, roughly transcribed by Donna:

  • It is important to keep the HR species and SQ species synchronized. At the few places where the default SQ frag table accounts for an ion and the HR species do not, or visa versa, we should reconcile the two.
  • The 'converted' HR frag table will likely be too confusing for typical users, as they aren't supposed to edit anything here. So this table should not have a button on the panel.
  • Jose suggested that perhaps there should be an option for adding in the squirrel sticks beyond the max HR fit m/z to the HR organic. Response from Donna: Folks can do that 'by hand' by making a new, duplicate Squirrel frag_organic that is blank up to the max HR m/z. Users can then manually add this extra organic to the HR organic time series, or the HR organic average stick spectra to plots themselves. For now, I think it a good thing that we keep HR organic as what we explicitly define it to be.
  • Add a small APES picture in the HR Results tab, Elemental Analysis group box?


Details:

Users should be aware that a few sulfate entries in the default list of all ions incorrect. Either the entry for the isotopic abundance is missing, or the parent ion is not the same formula as is given in the all ions table, or the entry refers to a wrong parent ion. I really hope the All HR ion group of Puneet, Delphine, Qi, and Niall will have this all straightened out!

END


Help

Are tutorials available?

Before using Squirrel, one should be familiar with the basic concepts of Igor. Several good Igor tutorials are available in the Wavemetrics/Igor Pro Folder/Learning Aids folder. You should know how to create, edit and find waves, and create, modify and find graphs.

Currently, there are 3 Squirrel presentations which can be downloaded:

  1. Squirrel overview power point presentation. The original form of this ppt was presented at the 2006 User's Meeting, and has been updated a few times since then.
  2. Squirrel pre-preprocessing power point presentation. This covers the m/z calibration and baseline fitting options. It is available as a ppt (4.4 MB)
  3. Squirrel post-preprocessing power point presentation. This covers the airbeam correction factor, DVa and DC marker calculations. It is available as a ppt (2.2 MB)

How do I report a problem with the ToF-AMS Analysis software? (Squirrel, Pika, Apes, etc)

There are a few places you should look before reporting any problems.

  • The Technical FAQ
  • The release notes of the version of Squirrel you are using and previous version release notes, if appropriate.
  • The coding to do list, because the feature you are dealing with may not be implemented yet or will be updated.

There are a few things you should try before reporting any problems:

  • Make sure the problem is replicable.
  • Isolate the problem to simplest, smallest case where the problem still occurs.
  • Gather the following (as appropriate):
    • the operating system of the computer, version of Igor, error message and symptoms
    • a screen shot of the problem or "Save Graph" if appropriate (e.g. if a graph looks odd)
    • the Igor experiment if it is small, or an example DAQ hdf if the problem is in regard to a specific file
  • Then put files info a folder you create on the Aerodyne FTP site. This ftp site is ftp://tofuser@ftp.aerodyne.com/ToF-AMS/SquirrelProblems/ and uses the same username and password as for downloading the ToF AMS software. Then fire off an email to Donna Sueper (sueper 'at' colorado.edu).

Please be aware that the latest versions of Squirrel will often have bugs fixed. Users should try upgrading to the latest Igor and ToF-AMS analysis software version to see if the problem persists.

How do I analyze AMS data with Squirrel?

The best resource is the wiki at http://cires.colorado.edu/jimenez-group/wiki/index.php/Field_Data_Analysis_Guide

How do I analyze AMS data with Pika?

The best resource is the wiki at http://cires.colorado.edu/jimenez-group/wiki/index.php/High_Resolution_ToF-AMS_Analysis_Guide

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