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anet-imagej

An ImageJ/FIJI plugin for running Anet, for processing images with ANNA-PALM and other models in ImageJ/FIJI.

anna-palm

Accelerating Single Molecule Localization Microscopy with Deep Learning

arduinocompressedsensing

A compressed sensing plugin for MicroManager to perform compressed sensing acquisitions

brightfield-drift-correction-3d

Acquire bright field images along with the super resolution data and use it to track drift in 3D with nanometer precision!

compressedsensingmicroscopy3d

Reconstruction notebooks for the paper "Simple 3D compressed sensing scheme for faster and less phototoxic fluorescence microscopy imaging"

deepcell

keras

Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano and TensorFlow.

loopextrusion

A tool to simulate loop extrusion in chromatin

lutorpy

Use torch in python for deep learning.

mnist-deep-learning-tutorial

pyspiraltap

Sparse Poisson Intensity Reconstruction ALgorithms

quickpalm

A 3D real-time PALM/STORM image processing plugin for ImageJ

rnntrajanalysis

sabate_et_al_tad_anchors

Python scripts to analyze loop extrusion from microscopy images and simulations

sagenb

Sage Notebook for super-resolution imaging automation

shareloc-collection

RDF Collection for ShareLoc.XYZ

shareloc-utils

Utility tools for ShareLoc.XYZ

shareloc.xyz

A platform for sharing localization microscopy data.

smlm-file-format

A portable and extendable file format for storing and sharing localization microscopy data.

smlm-viewer

taggedspot2csv

Convert Tagged Spot File (.tsf from MicroManager) to Comma Separated Values file(.csv for thunderSTORM)

thunderstorm

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging

voroquant

A 3D-voronoi-based python program to quantify SMLM data

zola-3d

Zernike Optimized Localization Algorithm for 3D single molecule localizations