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haiderriazkhan committed Feb 22, 2022
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CANDLE-J
========

CANDLE-J is a multi-language image denoising software designed as an [ImageJ](http://imagej.nih.gov/ij/) (64-bit) plugin and an open source alternative to the CANDLE MATLAB [program](http://www.bic.mni.mcgill.ca/ServicesSoftwareAdvancedImageProcessingTools/CANDLE/). CANDLE-J is very adept at processing deep in vivo 3D multiphoton microscopy images where the signal to noise ratio is low (SNR). The Collaborative Approach for eNhanced Denoising under Low-light Excitation (CANDLE) has been [tested](http://www.bic.mni.mcgill.ca/uploads/ServicesSoftwareAdvancedImageProcessingTools/candle.pdf) on synthetic data, images acquired on microspheres and in vivo images.
CANDLE-J is a 3D image denoising software designed as an [ImageJ](http://imagej.nih.gov/ij/) (64-bit) plugin and an open source alternative to the CANDLE MATLAB [program](https://sites.google.com/site/pierrickcoupe/softwares/denoising/multiphoton-image-filtering?authuser=0). CANDLE-J is very adept at processing deep *in vivo* multiphoton microscopy images where the signal to noise ratio (SNR) is low. The Collaborative Approach for eNhanced Denoising under Low-light Excitation (CANDLE) has been [tested](http://www.bic.mni.mcgill.ca/uploads/ServicesSoftwareAdvancedImageProcessingTools/candle.pdf) on synthetic data, images acquired on microspheres and *in vivo* images.

The denoising algorithms are written in Jython, Java and C. The C methods are accessed with the aide of the Java Native Access library. The Optimized Non Local Means Filter (ONLM) is the bottleneck of the CANDLE-J software and hence the ONLM algorithm is written as a multithreaded C program to improve performance. Additionally, the two C programs were compiled with the GCC optimizing option `-O3` turned on. The `-O3` option makes the compiler strive to improve the performance of the object code.

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**Important**
- For a Mac OS X; CANDLE-J should be used with the default `ImageJ` (64-bit) instead of the version named `ImageJ32` (32-bit). Both come bundled with the downloaded ImageJ zip file.

- In a Linux machine, use the version of ImageJ that appears with the default Linux executable icon. <img src="png/LinuxLogo.png" width="24" height="24" /> Using the wrong version causes an additional statement to appear in the ImageJ log window, `Error: Could not load pre-computed correspondence table`.
- In a Linux machine, use the version of ImageJ that appears with the default Linux executable icon: <img src="png/LinuxLogo.png" width="24" height="24" />. Using the wrong version causes an additional statement to appear in the ImageJ log window, `Error: Could not load pre-computed correspondence table`.



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