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Deconvolution Lab "Batch" Module

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Deconvolution Lab "Batch" Module

mirrownight
Hi,

Has anyone tried the "Batch" module in deconvolution lab with ImageJ ?
I have tried, but I cannot input multiple data sets, I don't know why.

When I select to input a folder, it told me there's no data input.
But if I select the tiff images, it says my input PSF has greater dimention than images.
Is there anyone can help?

Thanks,

Mirrownight
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Re: Deconvolution Lab "Batch" Module

bnorthan
Hi mirrownight

Is there any possibility that the PSF is 3D and the images are 2D??  Maybe
that is what the message "PSF has greater dimension than images" means.
Are you able to share the data??  If so I can try and run it.

Brian

On Wed, Mar 2, 2016 at 9:37 PM, mirrownight <[hidden email]> wrote:

> Hi,
>
> Has anyone tried the "Batch" module in deconvolution lab with ImageJ ?
> I have tried, but I cannot input multiple data sets, I don't know why.
>
> When I select to input a folder, it told me there's no data input.
> But if I select the tiff images, it says my input PSF has greater dimention
> than images.
> Is there anyone can help?
>
> Thanks,
>
> Mirrownight
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Deconvolution-Lab-Batch-Module-tp5015776.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Deconvolution Lab "Batch" Module

bnorthan
In reply to this post by mirrownight
Hi Morrownight

I just did a very quick test using Deconvolution Lab with Richardson Lucy
and batch mode.  My images were all .tifs, 8-bit, 2 dimensions (x,y), the
PSF was smaller than the image.  Everything worked fine.  Here are some
suggestions for trouble shooting...

1.  Check to make sure images and psf are indeed the same dimensions (no
extra channels, or z)
2.  Try making the images all .tif format
2.  Try making images and PSF the same pixel type (all 8-bit, all 32 bit).

On Wed, Mar 2, 2016 at 9:37 PM, mirrownight <[hidden email]> wrote:

> Hi,
>
> Has anyone tried the "Batch" module in deconvolution lab with ImageJ ?
> I have tried, but I cannot input multiple data sets, I don't know why.
>
> When I select to input a folder, it told me there's no data input.
> But if I select the tiff images, it says my input PSF has greater dimention
> than images.
> Is there anyone can help?
>
> Thanks,
>
> Mirrownight
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Deconvolution-Lab-Batch-Module-tp5015776.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Deconvolution Lab "Batch" Module

mirrownight
Hi, Brian

Thanks for your reply.

I've checked both the PSF and the images are all seperate image stacks each composed of 41 slices of 2D tiff images.  Hence, they have x-y dimension and z stack. Are the 3D image stacks not allowed to run Batch module in DeconvolutionLab ?

I make the PSF and the images the same x-y dimension (256x256 pixel), but it still doesn't work.
The link bellow is the data for test:

https://drive.google.com/file/d/0BzOF8t32YFytbEszdGJ3ZkZ2RUk/view?usp=sharing

Best regards,

Mirrownight
 

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Re: Deconvolution Lab "Batch" Module

mirrownight
This post was updated on .
 Hi, Brian

Here are the info of the PSF and images.

Thank you.


Mirrownight
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Re: Deconvolution Lab "Batch" Module

mirrownight
Here is the link of detailed description of my question.

https://drive.google.com/file/d/0BzOF8t32YFytQVBHbmh6dU1oaTg/view?usp=sharing

Thanks very much for the help.


Mirrownight
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Re: Deconvolution Lab "Batch" Module

bnorthan
Hi Mirrownight

I think that deconvolutionlab does not recognize the series of tif images
as a stack.  I got it working by doing the following

1.  Open each series as a stack by using file->import->image sequence
2.  I then resaved each stack as one 3D tif file, I saved them all in the
same directory.
3.  I then had a new directory, with 3 files, each representing a 3D stack
4.  Then I ran deconvolutionlab, and setting batch->'Input Folder' to point
to the new directory.

Let me know if the same process works for you

On Fri, Mar 4, 2016 at 1:43 AM, mirrownight <[hidden email]> wrote:

> Here is the link of detailed description of my question.
>
>
> https://drive.google.com/file/d/0BzOF8t32YFytQVBHbmh6dU1oaTg/view?usp=sharing
> <
> https://drive.google.com/file/d/0BzOF8t32YFytQVBHbmh6dU1oaTg/view?usp=sharing
> >
>
> Thanks very much for the help.
>
>
> Mirrownight
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Deconvolution-Lab-Batch-Module-tp5015776p5015797.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Deconvolution Lab "Batch" Module

mirrownight
Hi Brian

Thank you very, very, very much for the solution.

It's wierd for me that the PSF is still 2D tiff, but the input files should be 3D tiff for recognization.
I can not think of this idea.  But it's working now~


Thanks again for the help!!!


Mirrownight
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Re: Deconvolution Lab "Batch" Module

bnorthan
Hi Morrownight

Actually when I ran it both the PSF and Image were 3D

- I loaded the PSF as a series using the ImageJ import->sequence option, so
all the 2D slices were combined into a stack.
- DeconvolutionLab in batch mode is not able to detect the sequence...
itjust loads each file separately, thus they need to be combined into a
stack before hand.

On Sat, Mar 5, 2016 at 10:57 PM, mirrownight <[hidden email]> wrote:

> Hi Brian
>
> Thank you very, very, very much for the solution.
>
> It's wierd for me that the PSF is still 2D tiff, but the input files should
> be 3D tiff for recognization.
> I can not think of this idea.  But it's working now~
>
>
> Thanks again for the help!!!
>
>
> Mirrownight
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Deconvolution-Lab-Batch-Module-tp5015776p5015809.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Ash
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Re: Deconvolution Lab "Batch" Module

Ash
my input image size is 2048*2048*37 and psf size is 512*512*99....how should i resize it?do i have to do fft or ifft to get deconvolution result..the psf file that i have contain several beads....should i take average of all the beads in that file to deconvolution.... or just uploading the psf file with sveral beads is fine?
i am doing with deconvolution lab software...how should i proceed?
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Re: Deconvolution Lab "Batch" Module

bnorthan
Hi Ash

If you can share your image and psf I can try and help you.  From your
description I suspect your image contains multiple beads.  To use it as a
PSF you would have to crop out one bead.

Brian

On Mon, May 15, 2017 at 5:45 PM, Ash <[hidden email]> wrote:

> my input image size is 2048*2048*37 and psf size is 512*512*99....how
> should
> i resize it?do i have to do fft or ifft to get deconvolution result..the
> psf
> file that i have contain several beads....should i take average of all the
> beads in that file to deconvolution.... or just uploading the psf file with
> sveral beads is fine?
> i am doing with deconvolution lab software...how should i proceed?
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/Deconvolution-Lab-Batch-Module-tp5015776p5018724.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Ash
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Re: Deconvolution Lab "Batch" Module

Ash
hii
thank you for replying me..yes..i do have multiple bead...the psf has 99 frames and image has 37 frames....if i am cropping a single bead out then how should i adjust the size to make it compatible with the raw image???because raw images size is 2048*2048 and bead size is 512......if i crop out a single bead, then the bead file will become more smaller!!!

On Tue, May 23, 2017 at 8:00 PM, bnorthan [via ImageJ] <[hidden email]> wrote:
Hi Ash

If you can share your image and psf I can try and help you.  From your
description I suspect your image contains multiple beads.  To use it as a
PSF you would have to crop out one bead.

Brian

On Mon, May 15, 2017 at 5:45 PM, Ash <[hidden email]> wrote:

> my input image size is 2048*2048*37 and psf size is 512*512*99....how
> should
> i resize it?do i have to do fft or ifft to get deconvolution result..the
> psf
> file that i have contain several beads....should i take average of all the
> beads in that file to deconvolution.... or just uploading the psf file with
> sveral beads is fine?
> i am doing with deconvolution lab software...how should i proceed?
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/Deconvolution-Lab-Batch-Module-tp5015776p5018724.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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



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