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Number of citations per year for the bioinformatics software tool CLAHE

Tool usage distribution map

This map represents all the scientific publications referring to CLAHE per scientific context
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CLAHE specifications


Unique identifier OMICS_25627
Alternative name Enhance Local Contrast
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes




No version available


  • person_outline Stephan Saalfeld

CLAHE citations


Zebrafish skeleton development: High resolution micro CT and FIB SEM block surface serial imaging for phenotype identification

PLoS One
PMCID: 5722281
PMID: 29220379
DOI: 10.1371/journal.pone.0177731

[…] alyze the FIB SEM images, we first removed the effect of charging using the FFT signal of each image belonging to the stacks. Then the contrast levels of all the images were adjusted using the plugin Enhance Local Contrast []. The stacks were then manually aligned using the Align Slices command in Avizo. All the dense materials were surface-rendered using the Surface View command.The directionalit […]


Genetic drift and selection in many allele range expansions

PLoS Comput Biol
PMCID: 5728587
PMID: 29194439
DOI: 10.1371/journal.pcbi.1005866

[…] esults.To extract the local fraction of each strain per pixel, we first created binary masks for each fluorescence channel indicating if the corresponding E. coli strain was present. We utilized the “Enhance Local Contrast” (CLAHE) algorithm [] in Fiji [], an open-source image analysis platform, to help correct for inhomogeneities in background illumination. After applying the CLAHE algorithm, a c […]


FiloQuant reveals increased filopodia density during breast cancer progression

PMCID: 5626550
PMID: 28765364
DOI: 10.1083/jcb.201704045
call_split See protocol

[…] changes.” FiloQuant can then be found under “plugin → FiloQuant.” To run FiloQuant in ImageJ, users need to install the following dependencies: Enhanced Local Contrast (CLAHE.class;, Skeletonize3D.jar (, AnalyzeSkeleton.jar (; ), and Temporal-Color Code ( […]


The interaction of the bioinsecticide PA1b (Pea Albumin 1 subunit b) with the insect V ATPase triggers apoptosis

Sci Rep
PMCID: 5501856
PMID: 28687751
DOI: 10.1038/s41598-017-05315-y
call_split See protocol

[…] S ultramicrotome (Leica microsytems) and stained with lead citrate before examination with a Philips CM120 electron microscope. Afterwards, the contrast of the images was optimized using the PlugIn “Enhance Local Contrast (CLAHE)” on ImageJ software. […]


Butterfly gyroid nanostructures as a time frozen glimpse of intracellular membrane development

Sci Adv
PMCID: 5406134
PMID: 28508050
DOI: 10.1126/sciadv.1603119

[…] super-resolution fluorescence microscopy is used (, )], the need to image deep inside tissue, and limited contrast between biological agents and the aqueous environment, which requires biomarkers to enhance local contrast. The next most direct evidence is provided by rearing butterflies in a controlled fashion whereby the development is aborted at specific stages, followed by structural investiga […]


Role of nutrients and mTOR signaling in the regulation of pancreatic progenitors development

PMCID: 5444096
PMID: 28580286
DOI: 10.1016/j.molmet.2017.03.010
call_split See protocol

[…] or Counting Nuclei (ITCN) plug-in version 1.6 from the Center for Bio-Image Informatics ( after contrast enhancement using the Enhance Local Contrast (CLAHE) tool for ImageJ, “Contrast limited adaptive histogram equalization”, Graphics gems IV, Academic Press Professional, Inc. […]

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