ArticleMolecular biology of the cell2016
KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs.
Article in Molecular biology of the cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 130 papers.
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Who cites it
130 citing papers in PubMed, 237 citations in OpenAlex.
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- Cilia SubQ, a modular suite of pipelines for automated analysis of primary cilia and ciliary subdomains.bioRxiv : the preprint server for biology · 2026Article
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- TEP-1, a glial thioester protein is required for cilia organization and intraflagellar transport in ensheathed sensory neurons inMolecular biology of the cell · 2026Article
- Pathogenic KIF1A variants differentially disrupt axonal trafficking and impede synaptic development.bioRxiv : the preprint server for biology · 2026Article
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- Assessment of Lysosome Trafficking in iPSC-Derived Neurons Utilizing Time-Lapse Videos and TrackMate ImageJ Plugin Software.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Nucleosome unwrapping and PARP1 allostery drive affinities for chromatin and DNA breaks.Nature communications · 2025Article
- From cells to pixels: A decision tree for designing bioimage analysis pipelines.Journal of microscopy · 2025Article
- Inactivation of microtubule organizing center function of the centrosome is required for neuronal development and centriole elimination.bioRxiv : the preprint server for biology · 2025Article
- TEP-1, a glial thioester protein is required for cilia organization and intraflagellar transport in ensheathed sensory neurons.bioRxiv : the preprint server for biology · 2025Article
- Myosin VI controls localization of golgi satellites at active presynaptic boutons.Cellular and molecular life sciences : CMLS · 2025Article
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- DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins.Nature communications · 2025Article
- Genetically encoded and modular subcellular organelle probes reveal dysfunction in lysosomes and mitochondria driven by PRKN knockout.iScience · 2025Article
70 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of dynamic processes and are widely used in live-cell imaging. Although they contain the full range of dynamics, it is not straightforward to extract this quantitative information in a reliable way. Here we present two complementary, publicly available software tools, KymographClear and KymographDirect, that have the power to reveal detailed insight in dynamic processes. KymographClear is a macro toolset for ImageJ to generate kymographs that provides automatic color coding of the different directions of movement. KymographDirect is a stand-alone tool to extract quantitative information from kymographs obtained from a wide range of dynamic processes in an automated way, with high accuracy and reliability. We discuss the concepts behind these software tools, validate them using simulated data, and test them on experimental data. We show that these tools can be used to extract motility parameters from a diverse set of cell-biological experiments in an automated and user-friendly way.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.