For questions, comments or concerns please contact Imaging

6. Bruker TruLive3D Experiment


This page will guide through the steps to set-up a basic experiment.

1. Setting up an experiment

You have many possibilities to set-up an experiment with the Bruker TruLive3D. You can record a single z-stack at several time points, multiple z-stacks at several time points and you can also acquire bigger areas than the field of view by tiling the images together.

You can acquire data in a single channel with one or multiple laser lines on and simultaneously acquire images for two different emission channels, or you can create several channels for each laser line.

NOTE: if you only need one camera to acquire your images make sure you turn off the other one in the camera panel (unlink them and turn one off) otherwise both cameras will capture images which doubles the size of your data. 

CHANNEL:

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Z-STACK:

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EVENT and TASKS:

TRIGGER:

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SAVE YOUR SETTINGS:

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LuxBundle saving process:

SPECIAL CASES:

         2.  Visualize your data

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The image viewer in LuxBundle allows you to visualize the data frame by frame. It is not a 3D viewer, unlike Imaris viewer, but can give you an idea of what happened during your experiment at each time point. You can also play a movie of the z-stack. When you open the image viewer you can select the image data you want.

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3. Process the data

Finally, LuxBundle has an image processor function that allows you to do a few things to process your data. Click on the LuxProcessor tab.

For a complete overview of the capabilities of the Image Processor, please read the User Guide located in the little book icon on the top right corner of the LuxControl window.

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When your data is acquired, it automatically creates an imaris (.ims) header file along the Fiji Big Data viewer (bdv.h5) header files. However, depending on the size of your data set loading the images in imaris can take a very long time.

It also creates an ims folder where you can find the ims headers for the different stacks you acquired. The raw folder contains the raw data.

NOTE: As of May 2024, the ims headers created display the channels in opposite orientation making it impossible to visualize the two superimposed.

The image processor enables you to process your data stack by stack and create separate imaris header files. It also creates a mip folder with the maximum intensity projection of each stack. This can be useful in some cases to gather a quick view of the experiment and see if it looks good.

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Here, we will guide you through the steps to perform this task. For more information and potential debugging please refer to the User Guide in LuxBundle. You can also download the PDF version to read offline. And always ask the Beckman Center staff for guidance or in doubt!

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BigTIFF: If you want to save your data as TIFF files, check the box for "Copy images to BigTIFF".

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Revision #22
Created 9 August 2023 16:00:37 by Evolene Premillieu
Updated 5 December 2024 19:09:47 by Evolene Premillieu