Data Analysis

World Wide Series Seminar SpikeInterface is a unified Python framework for spike sorting. With its high-level API, it is designed to be accessible and easy to use, allowing users to build full analysis pipelines for spike sorting (reading-writing (IO) / preprocessing / spike sorting / postprocessing / validation / curation / comparison / visualization) with a few lines of code.

neuTube is an open source software for reconstructing neurons from fluorescence microscope images. It is easy to use and improves the efficiency of reconstructing neuron structures accurately. The framework combines 2D/3D visualization, semi-automated tracing algorithms, and flexible editing options that simplify the task of neuron reconstruction.

Two-photon calcium imaging is now widely used to infer neuronal dynamics from changes in fluorescence of an indicator. However, state of the art computational tools are not optimized for the reliable detection of fluorescence transients from highly synchronous neurons located in densely packed regions such as the CA1 pyramidal layer of the hippocampus during early postnatal stages of development.

Mice emit ultrasonic vocalizations (USV) to transmit socially-relevant information. To detect and classify these USVs, here we describe the development of VocalMat. VocalMat is a software that uses image-processing and differential geometry approaches to detect USVs in audio files, eliminating the need for user-defined parameter tuning.

3D Slicer is a software for medical image informatics, image processing, and three-dimensional visualization. It’s extremely powerful and versatile with plenty of different options. It is a great tool for volume rendering, registration, interactive segmentation of images and even offers the possibility of running Python scripts thought an embedded Python interpreter.

Colaboratory is a free Jupyter notebook environment that runs in the cloud. Your notebooks get stored on Google Drive. The great advantage is that you don’t have to install anything (however, for some features you need a Google account) on your system to use it.

NiBabel is a python package, under the NiPy project, that aims at unifying the process of opening different medical and neuroimaging file formats, including: ANALYZE,GIFTI, NIfTI1, MINC, MGH and ECAT as well as PAR/REC.

NiPy is an effort to make brain imaging research easier and more clear. This is implemented by providing a series of software that deal with file IO, analysis, and interfaces & pipelines.

BrainBrowser is a collection of open source, web-based 3D data visualization tools, mainly for neuroimaging studies. It is built using open technologies such as WebGL and HTML5. It allows exploration of cortical surface models (MNI and Wavefront OBJ, as well as FreeSurfer ASCII surface format) and volumetric MINC data.

Fiji is a distribution of ImageJ. The idea of the developers is to make the life of scientists easier by bundling ImageJ with nicely organised plugins and auto update function.