Pinned Repositories
aBeta_SMLM_analysisFIles
Files to format localization data from SRPipeline
anaDDA
anaDDA software for extracting transition rates from D distributions
big-fish
Toolbox for the analysis of smFISH images.
big-fish-examples
Notebooks to illustrate how BigFISH is working.
CajalCourse_2023
Code, references, and other resources relevant to the single-molecule tracking project
ChriSTORM
ImageJ scripts and macros for processing ThunderSTORM images
DDC
Correcting for Repeat localizations SMLM
DECODE
This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
Deep-STORM
Official implementation of Deep-STORM for dense 2D localization microscopy
DeepPALM-trained-models
Three trained models for an emitter density of 4, 6 and 9 emitters / µm^2 to be supplied to the CNN architecture published by Nehme et al.
VVvanL's Repositories
VVvanL/aBeta_SMLM_analysisFIles
Files to format localization data from SRPipeline
VVvanL/anaDDA
anaDDA software for extracting transition rates from D distributions
VVvanL/big-fish
Toolbox for the analysis of smFISH images.
VVvanL/big-fish-examples
Notebooks to illustrate how BigFISH is working.
VVvanL/CajalCourse_2023
Code, references, and other resources relevant to the single-molecule tracking project
VVvanL/ChriSTORM
ImageJ scripts and macros for processing ThunderSTORM images
VVvanL/DECODE
This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
VVvanL/Diinamic
Clustering analysis on single-molecule localization microscopy data
VVvanL/DL-AO
VVvanL/ExTrack
ExTrack MLE for diffusive noisy single-particle tracks
VVvanL/gramm
Gramm is a complete data visualization toolbox for Matlab. It provides an easy to use and high-level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.
VVvanL/lab-website-template
(Pre-release) An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more
VVvanL/Locan
Localization analysis software for super-resolution microscopy
VVvanL/matGeom
Matlab geometry toolbox for 2D/3D geometric computing
VVvanL/mathematical-methods-in-deep-learning-ipython
Python code (in the form of Jupyter ipython notebooks) to support the book "Math and Architectures of Deep Learning" (Krishnendu Chaudhury with Ananya Ashok, Sujay Narumanchi, Devashish Shankar).
VVvanL/matlab-schemer
Apply and save color schemes in MATLAB with ease.
VVvanL/NL2project_SmithLab
VVvanL/relative-enrichment
Code for Relative Enrichment analysis
VVvanL/scGEAToolbox
scGEAToolbox: Matlab toolbox for single-cell gene expression analyses
VVvanL/scRNA.seq.course
Analysis of single cell RNA-seq data course
VVvanL/slitflow
A Python framework for single-molecule dynamics and localization analysis
VVvanL/SMAP
VVvanL/smlm_clustering
Python scripts for molecular clustering analysis
VVvanL/Syn_Bot
Syn_Bot synapse calculation macro for FIJI
VVvanL/TARDIS-public
Public releases of TARDIS
VVvanL/TDA_applied_on_SMLM
This tutorail enables the use of persistent images as vector representation of structural properties of Sinlge Molecule Localization Microscopy (SMLM) to make further analysis like Principal Component Analysis (PCA)
VVvanL/TrackNTrace
TrackNTrace is an open source MATLAB framework for single molecule localization, tracking, and super-resolution applications written by Simon Christoph Stein and Jan Thiart from the University of Goettingen.
VVvanL/TRAIT2D
TRAIT2D is a cross-platform Python software package with compilable graphical user interfaces (GUIs) to support Single Particle Tracking experiments.
VVvanL/uvadlc_notebooks
Repository of Jupyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2021
VVvanL/ZeroCostDL4Mic
ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy