Marius Pachitariu and Carsen Stringer released a Python version of their Suite2p pipeline for two-photon imaging. So I decided to take this tool for a test drive with data collected from Scanbox. At the moment, Suite2p takes tiff and hdf5 files, so we first decided to write a function to convert *.sbx to *.h5 files. …
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New alignment and segmentation tools
Improved alignment and segmentation tools have now been released in the latest version of Scanbox, while retaining much of the functionality of the last version. sbxaligntool. The new alignment tool, shown below, adds batch processing of files, including the processing of eye and ball motion if those data are present. A region-of-interest (ROI) can optionally be…
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…
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Sbxsegmenttool: A simple GUI for off-line segmentation
Sbxsegmenttool is a simple GUI that replicates the same mechanism used in Scanbox’s online segmentation to assist in the segmentation of cells and/or processes in data that has already been collected. Sbxsegmenttool expects the images to have already been rigidly aligned. After loading an *.align file, the mean mean aligned image will be shown momentarily and then replaced by a…
Read MoreOnline cell segmentation in Scanbox
There is one hidden feature of Scanbox that has been around for some time, but I have not yet described. This feature allows for computer-assisted segmentation during an experiment. As you must already know, one way in which region of interests (ROIs) can be defined is manually. This process can be initiated by clicking on the Add button…
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Scanbox 