Aivia Software
Live import
- Hoyin Lai
- Aiden Maloney-Bertelli (Unlicensed)
- Luciano Lucas
Live Import is currently in Public Beta, please report any issues related to the usage of Live Import to Aivia.Support [at] leica-microsystems.com.
Interface
The Live Import dialog user interface is shown on the right. It has multiple options that let you specify the file dimensions and format. You can also choose to apply image fusion (for dual-view light sheet datasets) and add image calibration to the imported file.
Import parameters
The options in the Live Import dialog are as follows:
| Name | Description |
|---|---|
| Import Folder | Specifies the path to the acquisition folder |
| Result Name | Specifies the name of the imported file |
| Width | Specifies the width, or X dimension, of the acquired image in pixels |
| Height | Specifies the height, or Y dimension, of the acquired image in pixels |
| Z Planes | Specifies the Z dimension, or number of Z-slices in the acquired image |
| Time Points | Specifies the time dimension, or number of total time points in the acquired image |
| Channels | Specifies the number of image channels in the acquired image |
| Acquisition Order | Specifies the acquired image layout, or organization of its dimensions The acquisition order can be as follows (first specified dimension to last specified dimension):
|
| Bits Per Pixel | Specifies the bit-depth of the image; for 12- and 14-bit images, 16-bit is used |
| Fusion | This option is available for importing single-channel images only. Applies fusion to blend acquired image volumes together - this is particularly important for dual-view light sheet microscopes where two image volumes are acquired per time point; you can specify the blending direction - along the X, Y, or Z axes - and choose from two blending modes:
|
| X/Y Calibration | Specifies the lateral, or XY, resolution (unit per pixel) of the acquired image |
| Z Calibration | Specifies the axial, or Z, resolution (unit per Z frame) of the acquired image |
| Time Calibration | Specifies the temporal, or T, resolution (unit per time point) of the acquired image |
Controls
At the bottom of the dialog, there are six buttons:
| Name | Description |
|---|---|
| Simulator | Toggles the Live Import Simulator mode, which creates a simulated image sequence based on the parameters specified |
| File | Toggles single-file import with incrementally appended data (see the "Supported formats" section of this page) |
| Auto Seek | When enabled, the display will automatically jump to the most recently-converted image |
| Apply the Current Recipe | Applies the recipe that currently appears in the Recipe Console to the images as they are imported |
| Start | Starts Live Import mode (or with Simulator enabled, begins creation of the simulated image stack) |
| Cancel | Closes the Live Import window without starting Live Import |
|
| Live Import window |
Image fusion
Certain light sheet microscopes (e.g. mSPIM) can examine a sample from two opposing views to maximize image quality[1]. Reconstruction of the imaged sample for these microscopy platform requires fusion, or blending, of the two captured views to form a single image.
In Aivia, you can set Live Import to automatically fuse the two views when reconstructing the volume. The image below shows a zebra fish embryo imaged from View 2 using a light sheet microscope.
 |
Diagram of a dual-view imaging system with two opposed acquisition objectives (View 1 and View 2). In this example, the sample has a thickness of 800 microns, blending would occur in the 100 micron area on either side of the image midsection. |
In the Live Import window, select the blending axis (X, Y, or Z) in the first Fusion menu and the blending mode in the second. Blending will be applied across the whole dataset around the mid-section of the blending axis. There are two blending modes, Linear and Exponential, which correlate to the signal attenuation in the blend area.
- Linear: intensity signal attenuates at a constant rate across the blend area
- Exponential: intensity signal attenuates slowly at first before reaching a maximum rate at the midpoint and slowing again towards the other edge, as illustrated by the diagram on the right
Live Import currently supports image fusion of a single-channel image only.
|
| Intensity profile of exponential blend mode |
Using Live Import
Detailed information on how to use Live Import can be found on the How to set up Live Import page.
Acquiring real images
Before starting Live Import, make sure that you have sufficient hard drive space for storing the acquired images as well as the Aivia cache folder. When you are ready, go to File > Start Live Import and follow the instructions below:
- Specify the acquisition folder where the images will be saved to by either typing the folder path into the Import Folder textbox or by clicking on the Browse icon
next to the textbox, navigating to and selecting the folder, and clicking on Select Folder; make sure your acquisition software is set to save the files to the root of the specified folder and not in any subfolders. Specify the image dimensions in the Live Import dialog.
Make sure the image dimensions specified match the dimensions of the acquired files. Mismatched dimensions may lead to a malformed result image.
Start Live Import by pressing the Start button.
Do not start the image acquisition routine on your microscope until Live Import is active; starting acquisition prior to starting Live Import may lead to improperly formatted results.
- Start image acquisition on your acquisition software.
- Save the image when acquisition is complete and the full sequence can be viewed.
|
Select acquisition folder dialog |
References
- Huisken J and Stainier YR. (2007) Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). Optics Letters. 32(17):2608-10. doi:10.1364/OL.32.002608