The iTEM Solution Workflow
The iTEM Solution Tomography has the easiest workflow for achieving perfectly reproducible and reliable results from a tomography-suitable sample. Automated tilt series can be acquired on almost every modern TEM system – the list of supported TEMs is expanding constantly. The iTEM Solution Tomography comprises three main parts: acquisition, alignment and visualization
Acquisition of tilt series
The iTEM Solution Tomography allows the user to acquire a tilt series while automatically correcting focus changes, illumination conditions, specimen drift and mechanical instabilities of the goniometer by using live image tracking.
The goniometer of any particular TEM does not necessarily use real world coordinates. The image shift movements used for the autofocus, for example, might result in beam shift movements. This makes calibration and subsequent correction required. Normally, this is a time consuming and complicated task. The Solution Tomography, however, gives you a hands-on wizard guiding you through the calibration process in just a few minutes – reliable, reproducible and easy.
The acquisition that follows involves acquiring images while tilting the goniometer from -X° to +X° at a certain step width. The main goal is to keep the specimen centered, visible and focused. This is easy to accomplish by repeatedly tilting, tracking, focusing and acquiring. The automatic focus adjustment is fast and reliable. Automatic iTEM exposure control ensures acquisition conditions are optimal. This makes for fast image acquisition and low sample damage.
iTEM Solution Tomography acquisition supports the standard linear tilting mode (equal distance tilting steps). It also offers the Saxton scheme – a sinusoidal approach with finer steps while acquiring the images at the higher tilt angles giving increased resolution in the reconstructed tomogram.
The acquired tilt series can be stored as a standard multiple page TIFF file with all necessary image information and meta data (tilt axis, angle, shift, goniometer data, etc). This data is then used for alignment and reconstruction in the iTEM Solution Tomography.
In addition, stacks can be stored as an AVI file and played on any third party software.
Tilt series alignment
Tilt axis alignment is necessary after acquisition due to thermal effect, stage inaccuracies (backlash), specimen movement and so forth. There is observable drift between the individual stack images.
A comprehensive alignment routine aligns the images reliably along the tilt axis without requiring fiducial markers. Any necessary filters and morphing algorithms are applied automatically.
Additionally, any tilt series acquired using other tomography acquisition software, or manually with non-automated TEMs, can be imported and processed further. Supported file formats for stacks are TIFF, MTIFF, MRC, AVI and others.
Reconstruction and Visualization
A near perfect alignment is the primary prerequisite for perfect reconstruction. To reduce the waiting time, it is easy to choose one of the various reconstruction resolutions. The software selects the required settings automatically.
The final visualization step is done using SliceViewer and VoxelViewer, the fully integrated 3-D visualization tools. These tools offer display and navigation throughout all kinds of image stacks. Viewed with the SliceViewer, the reconstruction result (eg, FFT-based weighted back projection – WBP) enables the user to immediately assess the quality of the reconstructed tomogram.
The VoxelViewer offers various methods for 3-D object display: various projections (minimum, maximum, sum), isosurface (with triangulation) and a blending surface lets you easily generate useful images. Moreover, spatial positions and distances can be measured within the 3-D object.
The images generated using the VoxelViewer can be copied to the clipboard, exported as an animated AVI movie file or saved as multi-page TIF files.
There are two versions available of iTEM Solution Tomography upon request:
• Acquisition add-in: acquisition only
• Reconstruction add-in: alignment, reconstruction and visualization
The TEM must be equipped with a computer controlled (motorized) sample stage (goniometer) as well as an illumination and imaging system. Modifications necessary for establishing remote communications to the TEM are not included in the regular purchase price.