The general settings tab contains fields which let you name your current experiment and choose where and how the images you acquire are saved.
|A||Root.Path||Click 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.|
|B||Experiment Name||Titles the image set.|
|C||Experiment Type||Allows you to assign a type to your experiment depending on the type of images you plan to acquire.|
|D||File Format||SciScan allows you to choose from a variety of file formats including 16 and 32 bit multi-tiff and tiff-series as well as raw data formats.|
|E||Objective||Objectives 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 Analogue Output Tab for more info on setting up objectives.|
Files can be saved in two different file formats (raw binary or tiff file format) and two different data types (unsigned 16 bit integer or 32 bit single precision floating point).
Raw binary files should be used for fast streaming to harddisk. For analysis, raw binary files can be loaded directly into ImageJ using the provided Windows batch file. If you need assistance with importing raw binary files directly into your custom analysis routines (eg. Matlab, Python, ect.), please contact Scientifica.
Tiff files can be saved in the following configurations:
- Multi-tiff – A single tiff file containing multiple pages
- Tiff series – Multiple tiff files each containing a single image; tiff files are numbered and can be easily imported into ImageJ using the Import→Image Sequence command
Channels are arranged in the following manner:
- 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,…
Metadata is provided in two forms. First; a “configuration file” in which all the variables used during the recording are recorded as simple text. Second; relevant parameters are recorded as OME-Compliant XML metadata within the TIFF header. If recording the in the “raw” file format, the XML metadata is saved as a separate file alongside the image data.
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.