nanoTRON: a Picasso module for MLP-based classification of super-resolution data

Bioinformatics
Alexander AuerRalf Jungmann

Abstract

Classification of images is an essential task in higher-level analysis of biological data. By bypassing the diffraction-limit of light, super-resolution microscopy opened up a new way to look at molecular details using light microscopy, producing large amounts of data with exquisite spatial detail. Statistical exploration of data usually needs initial classification, which is up to now often performed manually. We introduce nanoTRON, an interactive open-source tool, which allows super-resolution data classification based on image recognition. It extends the software package Picasso with the first deep learning tool with a graphic user interface. nanoTRON is written in Python and freely available under the MIT license as a part of the software collection Picasso on GitHub (http://www.github.com/jungmannlab/picasso). All data files and code relevant for the review process of this paper can be accessed at https://datashare.biochem.mpg.de/s/iPBw9tj4OO9X4pC. Supplementary data are available at Bioinformatics online.

References

Mar 17, 2006·Nature·Paul W K Rothemund
Oct 16, 2009·Angewandte Chemie·Christian SteinhauerPhilip Tinnefeld
Mar 29, 2016·Nature Methods·Ralf JungmannPeng Yin
Mar 14, 2017·Chemical Reviews·Markus Sauer, Mike Heilemann
May 19, 2017·Nature Protocols·Joerg SchnitzbauerRalf Jungmann
Sep 7, 2017·Nature Reviews. Molecular Cell Biology·Steffen J SahlStefan Jakobs
Apr 17, 2018·Nature Biotechnology·Wei OuyangChristophe Zimmer
Apr 25, 2018·Nature Communications·Maximilian T StraussRalf Jungmann
Sep 13, 2018·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Alexander AuerRalf Jungmann
Jul 3, 2019·Nature Methods·John S H Danial, Ana J Garcia-Saez
Jul 10, 2019·Nature Methods·Chinmay Belthangady, Loic A Royer
Aug 2, 2019·Biochemical Society Transactions·Lucas von ChamierRicardo Henriques
Sep 14, 2019·Science·Aaron T Blanchard, Khalid Salaita
Sep 29, 2019·Nature Methods·Jervis Vermal ThevathasanJonas Ries
Oct 23, 2019·Nature Reviews. Genetics·Hamid Ramezani, Hendrik Dietz

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Citations

Jun 20, 2021·Nature Communications·Teun A P M HuijbenBernd Rieger
Jul 20, 2021·Frontiers in Genetics·Xian-Gan ChenHengling Chen

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Methods Mentioned

BETA
fluorescence microscopy
super-resolution microscopy

Software Mentioned

Python
sci
kit learn
Picasso
nanoTRON

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