General Settings Tab (Resonant)

The general settings tab contains fields which let you name your current experiment and choose where and how the images you acquire are saved.

Aroot.pathClick the folder icon to set the desired location for saved images. Each image set will be saved within a date-stamped folder complete with a copy of the .ini file in use at the time it was taken – capturing crucial information about how the image was acquired for later analysis
Bexperiment nameTitles the image set
Cexperiment typeAllows the user to assign a type to the experiment
Dfile formatOnly the 16bit raw data type is available for the resonant scanning system
EobjectiveObjectives are added and removed from this list via the .ini file. FOV and voltage settings for the scan system will change from objective to objective. See the Analog Output Tab for more info on setting up objectives.
Factive channelsSelect which channels are active, disabling will disable visualisation and acquisition. Light green indicates active.
Gchannel invertIndependently invert the signal (and therefore image) for each PMT, allowing the use of unidirectional positive or unidirectional negative PMT+Preamp combinations.

Saving Data

SciScan 1.1 introduces the option to save resonant scanning data in 16bit Multi-TIFF formats. Previously all resonant scanning data had to be saved as 16bit-RAW data. The TIFF format has the benefit of smaller file sizes in comparison to the raw data.

Raw Files

To make the raw data files more easily accessible, SciScan also writes a small macro alongside the raw data file which when run will automatically import the raw data into ImageJ. The Raw data can also be manually imported into either Matlab or ImageJ.

Please Note: Macro is only written if the ImageJ path specified in the .ini file points towards a locally installed version of ImageJ. Default path is: “C:\\Program Files (x86)\\ImageJ\\ImageJ.exe”

Final file path should take the following form: root.path/DateStamp/DateStamp_TimeStamp_ExperimentName/

Included in this folder will be:

  1. A copy of the data titled in the following format: DateStamp_TimeStamp_ExperimentName_ExperimentType.raw.
  2. A copy of the settings file used at time of acquisition.
  3. A windows batch file that will automatically import the data into ImageJ when run.
  4. A copy of the notebook contents at the time the recording finished.
  5. A XML file populated with OME-Compliant metadata

TIFF Files

TIFF images can be saved in three different formats;

  • Stacked – All channels are combined into a single image, stacked on top of each other; for example, a three channel recording of 256 by 256 pixels will be written as images of 256 by 768 pixels, whereby the first 256 lines correspond to channel 1, the middle 256 lines correspond to channel 2 and the bottom 256 lines correspond to channel 3.
  • Separate – Channels are split into separate images and written into separate multi-tiff files or separate tiff-series, whereby the file name indicates the channel number.
  • Interleave – Channels are split into separate images, but written into the same multi-tiff file or tiff-series as per the following example for a three channel recording:
    • channel 1 → images 1,4,7,10,…
    • channel 2 → images 2,5,8,11,…
    • channel 3 → images 3,6,9,12,…

When saving a TIFF file, the OME-XML metadata is included in the TIFF header.

When saving a TIFF file the following will be included in the data folder:

  • A copy of the data titled in the following format: DateStamp_TimeStamp_ExperimentName_ExperimentType.TIFF
  • A copy of the settings file used at time of acquisition.
  • A copy of the notebook contents at the time the recording finished.

The maximum size of a TIFF file is 4GB, because of this it may not always be possible to record your data in TIFF format if carrying out long or high resolution recordings. Resonant Scanners generate a lot of data very quickly, before recording an image, SciScan will estimate the final file size and force you to either change your parameters or to record the data in the 16-bit raw format if the file size would otherwise exceed 4GB.

TIFF File Size Limit Warning
TIFF File Size Limit

OME Compatibility

Both Resonant and Galvo versions of SciScan are now compliant with the Open Microscopy Environment (OME) XML Standard. Any TIFF saved from either version of the software will include OME compliant XML metadata while raw files will have a separate XML file saved along-side them.

For information on how to activate the generation of the XML metadata and edit the experimental settings, hardware settings and imaging parameter metadata see the OME Compatibility page.


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