CANDLE-J plugin released

[haider]

Hello everyone
The Collaborative Approach for eNhanced Denoising under Low-light excitation (CANDLE) is now available as an ImageJ plugin called CANDLE-J. CANDLE-J is instituted for the processing of 3D multi-photon microscopy images and is very adept for low signal to noise ratio typically encountered when imaging deep in scattered biological specimens.
Here is the link to the github repo that has installation instructions + information on usage:
https://github.com/haiderriazkhan/CANDLE-J
Also, here is the link to the CANDLE paper in Medical Image Analysis demonstrating its capabilities:http://www.bic.mni.mcgill.ca/uploads/ServicesSoftwareAdvancedImageProcessingTools/candle.pdf
Thank you and I hope people find this useful.
Haider Riaz KhanMcGill UniversityMontreal, Quebec    
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[haider]

Hello everyone

The Collaborative Approach for eNhanced Denoising under Low-light excitation (CANDLE) is now available as an ImageJ plugin called CANDLE-J. CANDLE-J is instituted for the processing of 3D multi-photon microscopy images and is very adept for low signal to noise ratio typically encountered when imaging deep in scattered biological specimens.

Here is the link to the github repo that has installation instructions + information on usage:
https://github.com/haiderriazkhan/CANDLE-J

Also, here is the link to the CANDLE paper in Medical Image Analysis demonstrating its capabilities:
http://www.bic.mni.mcgill.ca/uploads/ServicesSoftwareAdvancedImageProcessingTools/candle.pdf

Thank you and I hope people find this useful.

Haider Riaz Khan
McGill University
Montreal, Quebec

[Joel Sheffield]

This looks like a very useful tool.  I am sufficiently inexperienced that I
don't see how to download a version for the Win 7 computer that I am
using.  Can you provide some assistance?

Thanks



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*

On Sun, Jul 26, 2015 at 6:30 PM, HAIDER Riaz <[hidden email]>
wrote:

> Hello everyone
> The Collaborative Approach for eNhanced Denoising under Low-light
> excitation (CANDLE) is now available as an ImageJ plugin called CANDLE-J.
> CANDLE-J is instituted for the processing of 3D multi-photon microscopy
> images and is very adept for low signal to noise ratio typically
> encountered when imaging deep in scattered biological specimens.
> Here is the link to the github repo that has installation instructions +
> information on usage:
> https://github.com/haiderriazkhan/CANDLE-J
> Also, here is the link to the CANDLE paper in Medical Image Analysis
> demonstrating its capabilities:
> http://www.bic.mni.mcgill.ca/uploads/ServicesSoftwareAdvancedImageProcessingTools/candle.pdf
> Thank you and I hope people find this useful.
> Haider Riaz KhanMcGill UniversityMontreal, Quebec
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[haider]

Hello Joel

Thank you for your interest in CANDLE-J. Unfortunately, I have only released binaries for Mac OS X and Linux operating systems so far. As soon as I release a Windows version, I will post the update on this thread. For now, you would need either a Mac OS X or a Linux computer to try the program. Please let me know if you have any further questions.

Best Regards
Haider Riaz Khan  

[haider]

Hello Joel (and other ImageJ Windows users)

So I have finally released a binary for Windows operating systems as well. Please visit the Github repo and follow the instructions as before:
https://github.com/haiderriazkhan/CANDLE-J

I have also added sample images that you can download to test out the software.

Please let me know if anything is amiss.

Best
Haider Khan
 

[Kai Schleicher]

Hi Haider,

Thanks for this great plugin. Its works fine on imageJ 1.49v Java 1.6.0_24 [64-bit].

However, it does not work in my version of FIJI (ImageJ 2.0.0-rc-34/1.50a with java 1.6.0_26 (64-bit)). I downloaded and extracted the windows.zip file from github into the plugins folder of my FIJI and restarted FIJI. Unfortunately, CANDLE-J does not show up as a plugin.

Is there something on my side I could do to fix this?

cheers,
Kai

[Jan Eglinger]

Dear Kai, dear Haider,

I seemed to get CANDLE-J working in Fiji by doing the following:

    - introduced an underscore in the script file name: CANDLE_.py to
make it appear in the Plugins menu

    - moved the .dll files from the CANDLE-J folder to ./Fiji.app/lib/
to avoid an UnsatisfiedLinkError thrown by JNA

then it started to run but after a while, Fiji (to be precise, the JVM)
shut down without warning, leaving behind a log file like this:


#
# A fatal error has been detected by the Java Runtime Environment:
#
#  EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x000000006a84374e,
pid=8748, tid=9152
#
# JRE version: Java(TM) SE Runtime Environment (8.0_45-b15) (build
1.8.0_45-b15)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.45-b02 mixed mode
windows-amd64 )
# Problematic frame:
# C  [NoiseEstimation.dll+0x374e]
#


(I can send the whole log file to interested parties on request)

I tried to run with Java 6 and Java 8, but both Java versions led to
said access violation.

Any hints how to get the plugin running within Fiji are appreciated. It
would be nice to see it on an update site [1] some day, to make it easy
for users to install.

Cheers,
Jan

[1]: http://fiji.sc/Update_Sites


On 02.08.2015 19:53, Kai Schleicher wrote:

> Hi Haider,
>
> Thanks for this great plugin. Its works fine on imageJ 1.49v Java 1.6.0_24
> [64-bit].
>
> However, it does not work in my version of FIJI (ImageJ 2.0.0-rc-34/1.50a
> with java 1.6.0_26 (64-bit)). I downloaded and extracted the windows.zip
> file from github into the plugins folder of my FIJI and restarted FIJI.
> Unfortunately, CANDLE-J does not show up as a plugin.
>
> Is there something on my side I could do to fix this?
>
> cheers,
> Kai
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[haider]

Hi Jan & Kay

I just tested running CANDLE-J on Fiji. But I used a Mac OS X. Here is what worked for me:

- Like pointed out by Jan, you have to move the .dylib files (.dll for windows and .so for Linux) from the CANDLE-J folder to ./Fiji.app (the root directory for Fiji). I can perhaps release a separate version for Fiji , where this will not be required by using System.setProperty to specify where the shared libraries are.

- Then simply change the file name of CANDLE.py to CANDLE_.py . Again, as pointed out by Jan before.

Making these changes and restarting Fiji, CANDLE-J runs fine on my Mac OS X. I am not sure why Jan gets the fatal error on his Windows computer. The problem is very unlikely to be in the code. A quick google search reveals that the error is common and specific to Windows. Any Windows savvy person out there know anything that could help? I will try running CANDLE-J myself on a Windows computer soon.

I have not tested this on Linux either. I will try it out and let everyone know.

Best Regards
Haider

[Jan Eglinger]

Hi Haider,

On 04.08.2015 22:18, haider wrote:
 > I can perhaps release a separate version for Fiji, where this will
 > not be required by using System.setProperty to specify where the
 > shared libraries are.

May I suggest that instead of changing the library path (which might
interfere with files shipped by other update sites) you can just put the
libraries in a platform-specific subfolder [1] of the ./lib/ folder
before uploading using the ImageJ updater [2].
That way, users should automatically get the correct libraries for their
platform.

Regards,
Jan

[1]: http://fiji.sc/Uploading_plugins#File_organization
[2]: http://fiji.sc/How_to_set_up_and_populate_an_update_site



On 04.08.2015 22:18, haider wrote:

> Hi Jan & Kay
>
> I just tested running CANDLE-J on Fiji. But I used a Mac OS X. Here is what
> worked for me:
>
> - Like pointed out by Jan, you have to move the .dylib files (.dll for
> windows and .so for Linux) from the CANDLE-J folder to ./Fiji.app (the root
> directory for Fiji). I can perhaps release a separate version for Fiji ,
> where this will not be required by using System.setProperty to specify where
> the shared libraries are.
>
> - Then simply change the file name of CANDLE.py to CANDLE_.py . Again, as
> pointed out by Jan before.
>
> Making these changes and restarting Fiji, CANDLE-J runs fine on my Mac OS X.
> I am not sure why Jan gets the fatal error on his Windows computer. The
> problem is very unlikely to be in the code. A quick google search reveals
> that the error is common and specific to Windows. Any Windows savvy person
> out there know anything that could help? I will try running CANDLE-J myself
> on a Windows computer soon.
>
> I have not tested this on Linux either. I will try it out and let everyone
> know.
>
> Best Regards
> Haider
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[chin]

Hi Haider,

I noticed that the first 3 slices are black without any signal from the DenoisedImage. Could you tell me why those signal disappeared after doing the denoising treatment? Btw, does Candle-J also could be used for noisy stacks from clsm confocal microscopes? Thanks!

chin