Question

Answer

First you will need to make sure that you are using SmartCapture version 2.1 or newer. If you are using an older version contact us for details on how to upgrade. You can click on the 'contact us' link at the bottom of this page.

SmartCapture 2.1 introduced a new scripting command to export an image as a TIFF file. The new scriptable TIFF export has a number of advantages over the 'ExportTIFF' command that appears in the SmartCapture 'Image Processing' menu, these are:-

• You can specify the exact source of the data to be exported. E.g. you can export the raw data or any of the derived processed images.
• You have considerable control of the exported TIFF file options. E.g. you can specify whether to use PC or Mac byte ordering, you can export multiple images into separate TIFF files or a single multi image TIFF file.
• Image pixel data is exported faithfully (no normalisation is done).
• You can use scripting to automate the export process. E.g. If you have a number of images (say from a z-section) then a script can iterate over all of the images and export the lot in one go.

The best way to illustrate the use of the scriptable TIFF Export is by example.

• Start by downloading the example script and example filmstrip. This should give you the following files:

• Open the FilmstripPasteurZstack filmstrip in SmartCapture. This should open a filmstrip with several z-section images.
• Use the mouse to select the stacks in the filmstrip that you wish to export. Use the mouse together with the shift or command keys to extend or add to the selection.
• Next double click on the 'Export Selected As TIFF' Apple script file. This should open an AppleScript editor window displaying the example script.

• Click on the 'Run' button in the AppleScript editor window.

Going Further

Examine the script, It contains comments that should help explain how things are being done. Try making some simple modifications to the script.

To see how to add this script to either the button bar or the function keys read the FAQ on adding scripts to the button bar and function keys.

You can discover the format and parameters for the 'tiff export' command by reading the Apple Script dictionary entry for 'tiff export'. Do this from within the Apple Script editor, select 'Open Dictionary...' from the 'File' menu. When you get the 'Open' dialog, navigate you way to find the SmartCapture application, then examine the entry for 'tiff export' in the dictionary window.

Recommended Reading

AppleScript in a nutshell' by Bruce W Perry, published by O'Reilly available from Amazon.

Credits

The FilmstripPasteurZstack was kindly donated by Philippe Clerc of Genetique Moleculaire Murine, Institut Pasteur. Digital Scientific expresses it's thanks.

The stack crosses an ES cell nucleus which was differentiated for 3 days, and stained for DNA (DAPI) and for Xist RNA (red) by RNA FISH. These cells were derived from a female embryo and therefore have two X chromosomes, and which along cell differentiation start the process of X inactivation. The Xist probe detects a pinpoint of Xist expression on the elect active X chromosome. It detects a massive accumulation of Xist RNA on the elect inactive X chromosome. The stack nicely crosses both objects.

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