Journal
JOURNAL OF PHYSICS D-APPLIED PHYSICS
Volume 52, Issue 16, Pages -Publisher
IOP Publishing Ltd
DOI: 10.1088/1361-6463/ab0261
Keywords
super-resolution microscopy; ImageJ; Fiji; image analysis; image quality assessment; fluidics; single-particle analysis
Categories
Funding
- UK Biotechnology and Biological Sciences Research Council [BB/M022374/1, BB/P027431/1, BB/R000697/1, BB/S507532/1]
- UK Medical Research Council [MR/K015826/1]
- Wellcome Trust [203276/Z/16/Z]
- European Research Council [649101-UbiProPox]
- Centre National de la Recherche Scientifique (CNRS ATIP-AVENIR program AO2016)
- Engineering and Physical Sciences Research Council [EP/L504889/1]
- UK's Biotechnology and Biological Sciences Research Council
- Cancer Research UK [C1529/A17343]
- BBSRC [BB/P001440/1]
- MRC [MC_CF12266]
- 4 year MRC Research Studentship
- Swedish Research Council [621-20134685]
- UCL
- [MC_UU12018/7]
- BBSRC [BB/P001440/1, BB/R021805/1, BB/P027431/1, BB/M022374/1, BB/R000697/1] Funding Source: UKRI
- MRC [MR/K015826/1] Funding Source: UKRI
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Super-resolution microscopy (SRM) has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for SRM designed to combine high performance and ease of use. We named it NanoJ-a reference to the popular ImageJ software it was developed for. In this paper, we highlight the current capabilities of NanoJ for several essential processing steps: spatio-temporal alignment of raw data (NanoJ-Core), super-resolution image reconstruction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics). We expect to expand NanoJ in the future through the development of new tools designed to improve quantitative data analysis and measure the reliability of fluorescent microscopy studies.
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