All articles filed in scanbox
Surface sampling in Scanbox
Answering a request from colleagues in London, the upcoming version of the Scanbox firmware will allow users to change the depth of imaging on a line-by-line basis. Up to now, during volumetric imaging, users were allowed to change the setting of the electronically tunable lens (ETL) once per frame (during the transition from one frame to another). The…
Read MoreDisabling Knobby’s automatic reset
[Note: please do not use this feature yet — there are some bugs that need to be worked out. I will keep you posted.] Up to now starting a new Scanbox session from Matlab causes knobby will auto-reset, bringing all the position counters back to zero and clearing all its position memories. This is done because…
Read MoreNew Features in Scanbox 3.4
The latest release adds a few new features and fixes. A new panel called “Deadband & Alignment” offers the option to change some of the configuration variables on the fly. The deadband sliders allow to dynamically change the size of the left and right margins respectively, where the laser is blanked out. You can optionally…
Read MoreImportant enhancements in Scanbox 3.3 firmware
Good news! The latest Scanbox version in Github includes a few important improvements and fixes: The new firmware substantially decreases line jitter producing even shaper images. It removes the artifactual horizontal lines from the mean of bidirectional scanning acquisitions. It fixes a bug in the phase of the camera trigger signal. It checks for cases where no…
Read MoreLatest Scanbox Release brings cool performance improvements
The latest Scanbox release brings a major performance improvement. The main bottleneck in the acquisition loop consists of a function that re-arranges the incoming pixel stream into the images that are displayed and stored in real-time. This function now makes use of OpenMP to distribute the work among different physical cores available in your machine…
Read MoreA montage display for real-time display of volumetric data
By default, Scanbox displays the incoming image stream on its main window. Thus, during volumetric scanning, one sees the incoming images as depth is changing over time. If one is imaging only a handful of optical planes, it is difficult to see what is really going on. A different way to visualize the data in…
Read MoreA rolling average plug-in for scanbox
Scanbox offers a memory-mapped interface mechanism to expose incoming data to other processes. This facilitates a wide rage of customization by users that may want to display their data in different ways or do some on-line processing not currently supported by Scanbox. We previously provided one example of how a real-time histogram of the data can…
Read MoreReading scanbox files in Python
One quick way to get your data into Python is by using the Matlab API for Python. First, install the MATLAB engine API for Python by following he instructions here. You will need to install as administrator. Then, from your Python code you can simply do, as an example: This will read 50 frames starting at index…
Read MoreImprovements in alignment and segmentation tools
Two GUIs to align (sbxaligntool) and segment (sbxsegmenttool) two-photon imaging data from Scanbox were recently updated. Sbxaligntool allows users to perform alignment using rigid translation or a non-rigid deformation of the image stack. The tool now uses all the cores available in your computer along with the GPU. Rigid alignment can take place at near…
Read More
Scanbox 