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CANDLE specifications


Unique identifier OMICS_25878
Alternative name Collaborative Approach for eNhanced Denoising under Low-light Excitation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Java, MATLAB, Python
Computer skills Advanced
Version 1.02
Stability Stable
Maintained Yes


No version available



  • person_outline Pierrick Coupe

Additional information

CANDLE is available as an ImageJ JAVA plug-in at:

Publication for Collaborative Approach for eNhanced Denoising under Low-light Excitation

CANDLE citations


Wnt signaling controls pro regenerative Collagen XII in functional spinal cord regeneration in zebrafish

Nat Commun
PMCID: 5526933
PMID: 28743881
DOI: 10.1038/s41467-017-00143-0
call_split See protocol

[…] me-lapse images were denoised to improve image quality (enhance detail). Background noise, caused by the low signal to noise ratio, was removed from acquired time-lapse images using the ImageJ plugin CANDLE-J algorithm, which allows to remove the noise compartment while preserving the structural information with high fidelity. We verified that this procedure did not remove signals from processes o […]


An adaptation of astronomical image processing enables characterization and functional 3D mapping of individual sites of excitation contraction coupling in rat cardiac muscle

PMCID: 5703646
PMID: 29135437
DOI: 10.7554/eLife.30425.027

[…] image series carrying the upstroke phase of each resulting Ca2+ transient was extracted with custom code in MatLab. The resulting stacks data were de-noised with custom MatLab functions based on the ‘CANDLE’ de-noising algorithm (). A reference image containing the camera offset and the basal fluorescence was calculated by averaging two or three frames (14 or 21 ms) prior to electrical stimulation […]


The GPR 55 agonist, L α lysophosphatidylinositol, mediates ovarian carcinoma cell induced angiogenesis

Br J Pharmacol
PMCID: 4543616
PMID: 25989290
DOI: 10.1111/bph.13196
call_split See protocol

[…] ries (Wilmington, MA, USA) and placed in an incubator at 37°C, 40% humidity. On day 3, up to 8 mL of albumin was aspirated from a small hole made at the bottom of the egg and the hole was sealed with candle wax. Then an approximately 2 cm large window was cracked into the rounded part of the upright egg using Dumont tweezers (6) and the egg membrane was completely removed. The window was covered w […]


An assay to image neuronal microtubule dynamics in mice

Nat Commun
PMCID: 4175586
PMID: 25219969
DOI: 10.1038/ncomms5827

[…] EB3 comets that appeared on at least three consecutive frames. Polar plots were generated with IGOR software (WaveMetrics). Time-lapse movies recorded on scanning microscopes were de-noised using the CANDLE algorithm, a Matlab based software tool.The following parameters were measured: orientation (angle of comet deviation measured from the local neurite orientation set to 0°), density of dynamic […]


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CANDLE institution(s)
MNI, McConnell Brain Imaging Centre Montreal Neurological Institute, McGill University, Montreal, QC, Canada; LaBRI, Laboratoire Bordelais de Recherche en Informatique CNRS : UMR5800, Université Sciences et Technologies - Bordeaux I, Ecole Nationale Superieure d'Electronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Universite Victor Segalen - Bordeaux II, Talence, France; Instituto de Aplicaciones de las Tecnologias de la Informacion y de las Comunicaciones Avanzadas (ITACA) Universidad Politecnica de Valencia, Valencia, Spain; Montreal Neurological Institute McGill University, Montreal, QC, Canada
CANDLE funding source(s)
Supported by the Canadian Institutes of Health Research (CIHR, MOP-84360 and MOP-77567), Cda (CECR)-Gevas-OE016, a fellowship from the Deutscher Akademischer Austasch Dienst (DAAD) and a McGill Principal’s Award, a tier 2 Canada Research Chair, the Spanish Health Institute Carlos III through the RETICS Combiomed, RD07/0067/2001.

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