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Coding

SOFTWARE

HTP microscopy (2024)

In the work we demonstrated two common applications: (i) Extended-Depth-Of-Field (EDOF) imaging using a depth-insensitive PSF, and (ii) Snapshot 3D imaging using the Tetrapod PSF. In EDOF imaging, the resulting measurements can be used either directly or after a few iterations of Lucy-Richardson deconvolution

DBlink (2024)
A deep-learning-based method for super spatiotemporal resolution reconstruction from SMLM data.

DeepOM (2023)
A new computational method for optical genome mapping utilizing Deep Learning is presented, termed DeepOM.

Pattern Code (2023)
A model of OGM based on information theory, which enables the design of optimal labeling patterns for specific applications and target organism genomes. 

Live 3D measurement of telomere diffusion offers an effective method to investigate Chromatin dynamics. (2022)

  • CCCDO is a MATLAB package using ensemble MSD analysis in order to quantify chromatin dynamics.

  • Python code: Trajectory extraction, using localization results of DeepSTORM3D and the raw image sequence in order to reconstruct telomere trajectories, frame-by-frame.

DEEP-STORM 3D (2020)

This code implements two different applications of CNNs in dense 3D localization microscopy:

  • Learning a 3D localization CNN for a given fixed PSF (Tetrapod in this repository).

  • Learning an optimized PSF for high density localization via end-to-end optimization.

QAFKA (2021)

  • QAFKA is a deep learning based algorithm to estimate protein stoichiometry in cells by observing their blinking kinetics.

  • QAFKA repository contains google a colab notebook and a jupyter notebook for Anaconda.

VIPR (2020)
A pixel-wise phase retrieval software for pupil plane reconstruction/design.

ANOMALOUS DIFFUSION DATABASE (2019)

DEEP-STORM (2018)

A super resolution single molecule microscopy software. Deep-STORM in google colab as part of ZeroCostDL4Mic platform.

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