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Bruker TruLive3D main specifications The TruLive3D has 4 imaging channels at 405nm, 488nm, 561nm, 640nm.  The imaging objective is 25X 1.1NA water immersion. The magnification changer does not change the NA of the system.  The system is corrected fo...

This page contains some tips for sample preparation for the Bruker Trulive 3D. It is not exhaustive, it only gives a starting point for users on how to make their samples. Before planning an experiment, always check in with the Beckman center staff to ensure t...

Single Objective Light Sheet Microscope The Single Objective Light Sheet Microscope is also referred to as Oblique Plane Microscope or OPM. It is a custom design Light Sheet microscope that enables high resolution and can be used with standard coverslipped ...

Good news: Traditional sample preparation! The OPM sample holders are similar to that of other commercial microscopes. Slides, round dishes and multi-well plates can be used. There is nothing different for your sample preparation so far. 

The Single Objective Light Sheet Microscope is a custom-designed microscope and is a VERY sensitive instrument. It is very easy to bump components out of alignment. For this reason, you will not be allowed to use it in autonomy. There are no trainings provide...

OPM Data The data generated by the OPM is in TIFF format. Whether you acquire a single image or a z-stack, you will get a single TIFF file containing all the images. The software also saves an "experiment" file in Yaml format that contains all the experime...

The Fiji plugin for annotating movies with custom arrows was developed by Stephan Daetwyler, Carl D.Modes and Reto Fiolka at UT SouthWestern. To read about it and acknowledge the authors, please refer to this publication.

Complete instructions for plugin installation can be found in this publication. The GitHub page with the source code can be found here. Here is a Youtube video with a tutorial to install and use the plugin.

The data generated by the Bruker TruLive3D contains a Fiji header named bdv.h5.  Fiji is an open source software that can be very powerful to view, process and render your data. You should really explore its possibilities! When you install Fiji (ImageJ) it c...

This page is a guide to set-up an experiment with the OPM.  All experiments on the OPM will be done under the supervision of the Beckman staff and you will get help with processing the data to make it ready to analyze. Turning the system on   Inserting the...

  If you are using Python for image analysis already, Napari is a great package to help you visualize and render your data!   Documentation and downloads can be found on this page. Below is an example of 3D rendering in Napari.     Napari offers a lot...

To load an image in Imaris Make sure you are in the Arena view (see above). Click on Observe Folder, then select the folder with your images in the dialog box that pops up. If you have not opened the file before, the file will likely have an ND2 extensi...

This page explains how to use intensity-based thresholding (the traditional method) to segment cells. For this example, we will segment some nuclei which have been labeled with DAPI. In the Surpass view, click on the Surfaces icon in the left panel to creat...

This section explains how to use the ML segmentation tool in Imaris.  In the Surpass view, click on the Surfaces icon in the left panel to create a new Surface. A wizard dialog box will appear on the bottom left of the screen. On this page:  Unselect C...