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 More

Spikefinder: the Vanilla algorithm

Over the last few months, the Spikefinder challenge has provided a playing ground for colleagues to offer ideas about how to estimate the spiking of individual neurons based on the measured activity of fluorescent calcium indicators. The challenge was for people to come up with strategies that beat the performance of state-of-the-art algorithms, STM & oopsi. A good number of algorithms were able…

Read More

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 More