Source 1primary paper2019Journal of Physics D Applied Physics
Toolkit/ImageJ
ImageJ
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
ImageJ is a versatile and powerful tool for quantitative image analysis in microscopy.
Usefulness & Problems
Why this is useful
ImageJ is presented as a general quantitative microscopy image-analysis platform. In this article it is positioned as a base environment for SMLM analysis workflows.; quantitative image analysis in microscopy; single-molecule localization microscopy analysis
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ImageJ is presented as a general quantitative microscopy image-analysis platform. In this article it is positioned as a base environment for SMLM analysis workflows.
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quantitative image analysis in microscopy
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single-molecule localization microscopy analysis
Problem solved
It gives users an accessible, open-source way to perform microscopy image analysis, including automated and quantitative analysis tasks.; provides an open-source platform for microscopy image analysis
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It gives users an accessible, open-source way to perform microscopy image analysis, including automated and quantitative analysis tasks.
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provides an open-source platform for microscopy image analysis
Problem links
provides an open-source platform for microscopy image analysis
LiteratureIt gives users an accessible, open-source way to perform microscopy image analysis, including automated and quantitative analysis tasks.
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It gives users an accessible, open-source way to perform microscopy image analysis, including automated and quantitative analysis tasks.
Published Workflows
Objective: Use the ImageJ/Fiji ecosystem for end-to-end single-molecule localization microscopy analysis, spanning localization, image reconstruction, and downstream postprocessing.
Why it works: The abstract states that multiple plugins and macros together cover the major SMLM analysis steps from localization through reconstruction to postprocessing, enabling automated and quantitative analysis within the ImageJ/Fiji environment.
single-molecule localizationimage reconstructiondensity analysisimage registrationresolution estimationImageJ/Fiji-based image analysisplugin and macro extension workflow
Stages
- 1.Single-molecule localization(broad_screen)
The abstract identifies single-molecule localization as the first covered step in the SMLM analysis sequence.
- 2.Image reconstruction(functional_characterization)
The abstract states that the tools cover image reconstruction after single-molecule localization.
- 3.SMLM data postprocessing(secondary_characterization)
The abstract explicitly lists postprocessing as the downstream stage following localization and reconstruction.
Selection: postprocessing tasks such as density analysis, image registration, or resolution estimation
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete measurement method used to characterize an engineered system.
Mechanisms
automated image processingimage reconstructionimage registrationquantitative image analysisresolution estimationsingle-molecule localizationTechniques
Functional AssayTarget processes
localizationImplementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensor
It requires ImageJ software and, for SMLM-specific tasks, associated plugins or macros. No hardware or wet-lab prerequisites are described in the abstract.; use depends on software plugins or macros for specific SMLM tasks
Independent follow-up evidence is still limited. Validation breadth across biological contexts is still narrow. Independent reuse still looks limited, so the evidence base may be fragile. No canonical validation observations are stored yet, so context-specific performance remains under-specified.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
Fiji is a valuable and powerful extension of ImageJ for image processing.
Especially the image processing package Fiji is a valuable and powerful extension of ImageJ.
ImageJ is an open-source, platform-independent tool for quantitative image analysis in microscopy.
ImageJ is a versatile and powerful tool for quantitative image analysis in microscopy. It is open-source software, platform-independent
ImageJ/Fiji can be used for automated and quantitative data analysis in SMLM.
This article describes how ImageJ/Fiji can be used for image analysis... to explore the possibilities of ImageJ/Fiji for automated and quantitative data analysis.
SMLM plugins and macros in the ImageJ/Fiji ecosystem cover single-molecule localization, image reconstruction, and postprocessing tasks including density analysis, image registration, and resolution estimation.
These novel tools cover the steps from single-molecule localization and image reconstruction to SMLM data postprocessing such as density analysis, image registration or resolution estimation.
Approval Evidence
1 source3 linked approval claimsfirst-pass slug imagej
ImageJ is a versatile and powerful tool for quantitative image analysis in microscopy.
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capabilitysupports
ImageJ is an open-source, platform-independent tool for quantitative image analysis in microscopy.
ImageJ is a versatile and powerful tool for quantitative image analysis in microscopy. It is open-source software, platform-independent
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use casesupports
ImageJ/Fiji can be used for automated and quantitative data analysis in SMLM.
This article describes how ImageJ/Fiji can be used for image analysis... to explore the possibilities of ImageJ/Fiji for automated and quantitative data analysis.
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workflow scopesupports
SMLM plugins and macros in the ImageJ/Fiji ecosystem cover single-molecule localization, image reconstruction, and postprocessing tasks including density analysis, image registration, and resolution estimation.
These novel tools cover the steps from single-molecule localization and image reconstruction to SMLM data postprocessing such as density analysis, image registration or resolution estimation.
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Comparisons
Source-stated alternatives
Fiji is described as a valuable and powerful extension of ImageJ.
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Fiji is described as a valuable and powerful extension of ImageJ.
Source-backed strengths
open-source; platform-independent; supports automated and quantitative data analysis
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open-source
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platform-independent
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supports automated and quantitative data analysis
Compared with Fiji
Fiji is described as a valuable and powerful extension of ImageJ.
Shared frame: source-stated alternative in extracted literature
Strengths here: open-source; platform-independent; supports automated and quantitative data analysis.
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Fiji is described as a valuable and powerful extension of ImageJ.
Ranked Citations
- 1.