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  Batch Processing

If you to want to manipulate many spectra using the same commands and/or the same parameters, you can use two iNMR shortcuts. The first is to visualize the FIDs as overlays into a main window. After processing the main spectrum, open the Overlay Manager and hit the button: “Batch Processing”. This shortcut only works with FIDs. A more versatile option is the “Process Folder” command. The requirement, in this case, is that all your spectra must be into the same folder, at the same level. You choose only one, any one, perform the necessary processing, then the command “Process Folder” will do the rest. The spectrum you have chosen will be used as a model. If processing parameters already exist in the rest of the folder, they will be deleted. If the spectra are already transformed, they are discarded and processing restarts from the FID every time. The “Process Folder” command can be used at any moment and how many times you need. For example, you can FT and phase correct the model spectrum, then process the folder. After adjusting the phase individually to each spectrum, you apply baseline correction, then process the whole folder with automatic TMS-referencing. In a third stage you can reduce a spectrum in bins and finally reduce in bins the whole batch.

You have enough control over which processing is performed. For phase correction you have four options:

  1. Respect the parameters already existing in external files (i.e: iNMR does nothing).
  2. Copy the parameters from the model file (the foremost window, normally the one you have worked on).
  3. Perform the standard automatic phase correction. Choose it when the spectral width is narrow, or the baseline is not flat, or when the baseline is perfectly corrected.
  4. Perform the metabolomic automatic phase correction. Choose it when the spectral width is large, the baseline is flat but non-zero, the signal are concentrated at the center of the spectrum. Neither method will work if the corrected spectrum contains peaks of both sign.

You also have three options for changing the scale reference:

  1. Respect the scale already existing in external files (iNMR does nothing).
  2. Copy the reference from the model file.
  3. Let iNMR search for the TMS (or TSP) signal, and reference each spectrum against it. In this case you can specify the range where to search in. iNMR will recognize as TMS the highest peak into that range. This function is applied to all spectra, including the model spectrum. You are allowed to specify a different reference, by writing a non-zero ppm value into field on the left.

Some processing functions are applied, yet do not appear into the dialog: suppression of signals, linear prediction, polynomial baseline correction, symmetrization, bucketing. They are always copied from the model spectrum. There is a partial exception in the case of baseline correction of 1D spectra. The manual baseline correction is not copied into the external files. The automatic polynomial correction is instead performed with the same parameters. The simpler “straight line fitting” needs to be applied explicitly.
A final option (“copy integral regions”) is equivalent to the combination: Copy Integrals + Paste.

Remember that, with the manual phase correction, you can change the phase simultaneously to all the overlays present into a window.


Pseudo-2D and Windowless Overlays

Even the fastest computer slows down a lot when there are too many open windows. You have two options to avoid this situation:

  1. Store the processed spectra into a single matrix, where they can be easily inspected. It is required that the file names make a simple arithmetic progression. You have the option to specify the lowest number from which the progression will start. The windows containing the experimental spectra are closed after processing (the new parameters are saved into each document). 2D and 3D spectra ignore this option.
  2. Create Windowless overlays. You are not creating any new file: each spectrum will still be saved into its own file, but they will be visualized as overlays over your designated (model) spectrum. The difference between a standard overlay and a windowless one is minimal. The former can behave as overlay in many windows simultaneously, while the latter can't. If you only want to create windowless overlays (without performing batch processing), uncheck the option “Overwrite Existing Processing”. When iNMR opens a file containing more than 30 standard overlays, automatically converts them into windowless ones.

See also

Exporting Data

Referencing the Frequency Scale

Color in iNMR

Metabolomic Toolbox