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Data Analysis
Deep Cinac
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.
Jun 6, 2020
1 min read
Calcium Imaging
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Software
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Behaviour
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Data Analysis
VocalMat
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.
May 27, 2020
1 min read
Software
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Behaviour
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Data Analysis
3D Slicer
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.
May 22, 2020
1 min read
Software
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Data Analysis
Colaboratory
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.
May 10, 2020
1 min read
Software
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Data Analysis
NiBabel
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.
André Maia Chagas
May 5, 2020
1 min read
Data Analysis
Nipy
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.
André Maia Chagas
May 5, 2020
1 min read
Data Analysis
BrainBrowser
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.
André Maia Chagas
Jan 1, 0001
1 min read
Data Analysis
Fiji
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.
André Maia Chagas
Jan 1, 0001
1 min read
Data Analysis
PySpace
PySpace is a signal processing and classificiation environment for Python. Modular software for processing of large data streams that has been specifically designed to enable distributed execution and empirical evaluation of signal processing chains.
André Maia Chagas
Jan 1, 0001
1 min read
Data Analysis
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Software
Tensor Flow
Google has packaged their deeplearning machine learning tools and made it open source. The project is called tensorflow, and is available here. Some nice tutorials on the website, so that with a bit of patience, people can start to deep their toes into machine learning!
André Maia Chagas
Jan 1, 0001
1 min read
Data Analysis
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