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.

The Live Import function imports images (2D or 3D) as they are being acquired on a microscope and converts the file into Aivia's multi-resolution format for 3D display in real-time. The function looks for files being added into a user-specified acquisition folder and assembles the result sequence in Aivia. When acquisition is complete, you can save the compiled file in Aivia TIFF format without additional conversion steps.

To launch Live Import, go to File > Start Live Import.

On this page:

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): XYZCT XYCZT CXYZT ZXYCT ZCXYT ZCXYT CZXYT
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: Linear Exponential
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

Supported formats

Live Import automatically updates the displayed volume in 3D View when the acquisition software completes a full frame of image acquisition, composed of a single time point with all Z-slices and channels. Live Import supports use cases with one file or multiple files per acquisition; different file types are supported for each acquisition method.

Acquisition mode	Supported formats	Description
Multiple files	TIFF, RAW, DAT (tested) Other formats with native Aivia support (untested)	The acquisition software creates a single file per Z plane, per time point, and/or per channel. When the files are written to disk, Live Import collects them in memory to build a single time point. Once a full time point is in cache, Aivia will convert the volume into Aivia's multi-resolution format and display the result in 3D View.
Single file	SLD (3i), TIFF	The acquisition software creates a single file containing the full structure of the file and updates the file as images are acquired on the system. Live Import will convert the volume and display the result in 3D View as new time points are added into the file.

Acquisition mode

Supported formats

Description

Multiple files

TIFF, RAW, DAT (tested)

Other formats with native Aivia support (untested)

The acquisition software creates a single file per Z plane, per time point, and/or per channel. When the files are written to disk, Live Import collects them in memory to build a single time point.

Once a full time point is in cache, Aivia will convert the volume into Aivia's multi-resolution format and display the result in 3D View.

Single file

SLD (3i), TIFF

The acquisition software creates a single file containing the full structure of the file and updates the file as images are acquired on the system. Live Import will convert the volume and display the result in 3D View as new time points are added into the file.

Performance expectations

Actual performance (i.e. how quickly Aivia will display a 3D time point after it is written to disk) will vary significantly based on the hardware used and image dimensions. For a PC with two 1 TB SSD drives, 128 GB of RAM and a modern (2018) high end Intel CPU Aivia can process and display up to 7 GB of data per minute (test image dimensions: 1881x821x844 16 bit, 2.5 GB per time point). Thus, for the test image mentioned Aivia will read, process and display a new time point every 20 seconds approximately.

Simulator mode

You can perform a test run of Live Import using the Simulator option in the Live Import window. In Simulator mode, Aivia will initiate a simulated acquisition sequence generating an artificial image volume based on the image dimensions specified once you click Start in the Live Import window. The simulated image will be displayed in Aivia only and will not be stored in the specified acquisition folder.

You can terminate the simulation early by going to File > Stop Live Import to stop Live Import.

Image credits

Jiaye (Henry) He, Jan Huisken Lab, Morgridge Institute for Research, Madison WI

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

Interface

Import parameters

Controls

Image fusion

Using Live Import

Acquiring real images

Supported formats

Performance expectations

Simulator mode

Image credits

Related articles

References

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