The Zebrafish Activity Prediction Benchmark measures progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain.
navigate - open source light-sheet microscope controls
Detect morphological motifs, such as blebs, filopodia, and lamellipodia, from 3D images of surfaces, particularly images of cell surfaces.
Vectorial ray tracing software for light-sheet microscopes
Python toolkit for 2D/3D image processing using CPU or GPU
A fully open-source system for prospective optical gating in 3D fluorescence light sheet cardiac imaging
Crown-like Structure Detection and Segmentation in 3D Light-sheet Microscopy Imaging with Mask R-CNN
Stripe artifacts elimination of LSFM images using deep learning method
Measuring laser intensity underwater in a sample chamber with an open-hardware solution
A pipeline for processing and analysis of light-sheet microscopy images.
Matlab app to destripe, using Pierre Weiss VSNR, and deshake, using Guizar-Sicairos, Thurman, and Fienup Efficient subpixel image registration algorithms
Python code for merging and refinement of detected neurons in large 3D stacks
Growth Hormone effect on Cartilage Growth Plate; Light-Sheet Microscopy; Pseudocoloring | Projects I started and still working on in Andrei Chagin Lab | Karolinska Institutet
Collection of scripts for running data processing of light sheet data
Analysis and simulation toolkit for thermal lensing effects in two-photon light-sheet microscopy. Includes experimental data processing (Python) and beam propagation simulations (Julia). Part of the preprint: Thermal Lensing Effects in Two-Photon Light-Sheet Microscopy.
Multi-Orientation MAXWELL: A novel approach to three-dimensional super resolution mapping of X-ray excited, visible light emitting fluorophores using the X-ray Light Sheet Microscopy technique MAXWELL.
Bei Liu's personal website
cells activity, voxel_to_volume in tissue conversion, density and stats
Modular, high-resolution light-sheet microscopes for accessible 3D subcellular imaging.
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