Thanks to the work of João Couto, Suite2p now reads *.sbx files. I just processed some of our data and it works nicely. You can download Suite2p from here. Some of the metadata are currently missing, as they are stored in a Matlab’s object that is not easily read in Python, but I will be…
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Online, pixel-wise image processing with a Scanbox plugin
Sometimes you need your results right away. One example is when subsequent experiments are tailored to the properties of neurons in the population at hand. Here is a simple Scanbox plugin that computes an orientation map preference on a pixel-by-pixel basis as the data are collected. The variable mmfile.Data.header(4) indicates if a stimulus is being…
Read MoreThe Mesoscope Panel
If you are already familiar with Scanbox on the NLW standard system, you will find it very natural to use the new options available in the mesoscope. When Scanbox is configured to operate the mesoscope, you will find a new panel giving access to the features that go beyond those of the standard configuration: Here is…
Read MoreUsing Suite2p with Scanbox
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. …
Read MoreSupport for Phenosys Speedbelt Linear Treadmill
Scanbox now provides a direct interface to Phenosys’ speedbelt. Once the speedbelt is connected via the USB to the computer it will show up as a COM port on the Device Manager. To acquire input from the treadmill, simply define the speedbelt_com configuration variable specifying the corresponding COM port. Within the Scanbox “Treadmill and Encoder”…
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Mesoscope features: real-time panoramas, ROI selection, zoom/pan, and dynamic ROIs
Here are some of the features we have been developing to make it easy to build panoramas, pick regions-of-interest, and to visualize ROI location and data during acquisition using the NLW Mesoscope (aka the Kraken) on the latest version of Scanbox. The video below shows a brief demo of the following: The automatic creation of…
Read MoreFinding the optimal sample clock phase
Some time ago we talked about the advantages of synchronizing the digitizer sample clock to the laser. Our new system incorporates an on-board PLL multi-phase clock that allows Scanbox to automatically measure the contrast in a test image as a function of sample phase delay and select the optimal value for your setup. A typical measurement…
Read MoreIntrinsic & epi-fluorescence imaging using the port camera
Some colleagues have asked about the possibility of integrating imaging acquisition from the port camera to do intrinsic and/or epi-fluorescence imaging ahead of targeting a region of interest with two-photon experiments in Scanbox. We have now added this option to Scanbox. To use this option you will need to wire the I2C port on the…
Read MoreNew 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 MoreKnobby gets a wireless sister
A welcome addition to the family: Knobby Tablet. Works on any Android tablet. Makes it easier to move the microscope from anywhere in the Lab. More details soon!
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