FIJI thinks my greyscale image stack is a coloured image?

[Mr_Sonky]

Hi all, I've got a simple question. Why does FIJI open my stack of grayscale images as a colour image?? I know it does this because of the letter "c" in place of the "play" button when we want to scroll between slices in a stack. Also it does this annoying thing where it colour codes i.e. Slice #1: Red, Slice #2: Green..etc.. this goes on to Slice #6: Yellow.. and Slice 7 onwards to Slice 361 remains gray (its original colour). All images are acquired by a monochromatic sensor so I know the colour is not real.

When I apply a 'Grays' LUT, it either doesn't save or I wants me to convert to 8-bits first. But doing so doesnt solve the problem of the "c" slider.  In addition, I found that when the "c" slider is present, I can't adjust the Brightness/Contrast for all slices whereas before I normally could with a standard greyscale stack. When I tried opening the SAME image file using ImageJ, it opens normally without the pseudo-colouring the first 6 slices. Everyhting else also works when opened in ImageJ (as opposed to FIJI)



The image on the right and left essentially the same opened in different programs.. Would really appreciate if someine can explain to me how to stop this annoying behaviour!

[LIM Soon Yew John (IMB)]

Hi Sonky,

Are you using FIJI (ImageJ2)? If yes, you can try to turn off the SCIFIO under Edit>Options>ImageJ2. I encounter an issue that FIJI (ImageJ2) did not open my RGB image correctly but it works again after I turn off SCIFO.

Another thing that you can try is go to Image>Hyperstacks>Stack to Hyperstack..., set the correct number of slices and channel.

Best Regards,
John

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________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Mr_Sonky [[hidden email]]
Sent: Thursday, August 07, 2014 9:56 AM
To: [hidden email]
Subject: FIJI thinks my greyscale image stack is a coloured image?

Hi all, I've got a simple question. Why does FIJI open my stack of grayscale
images as a colour image?? I know it does this because of the letter "c" in
place of the "play" button when we want to scroll between slices in a stack.
Also it does this annoying thing where it colour codes i.e. Slice #1: Red,
Slice #2: Green..etc.. this goes on to Slice #6: Yellow.. and Slice 7
onwards to Slice 361 remains gray (its original colour). All images are
acquired by a monochromatic sensor so I know the colour is not real.

When I apply a 'Grays' LUT, it either doesn't save or I wants me to convert
to 8-bits first. But doing so doesnt solve the problem of the "c" slider.
In addition, I found that when the "c" slider is present, I can't adjust the
Brightness/Contrast for all slices whereas before I normally could with a
standard greyscale stack. *When I tried opening the SAME image file using
ImageJ, it opens normally* without the pseudo-colouring the first 6 slices.
Everyhting else also works when opened in ImageJ (as opposed to FIJI)

<http://imagej.1557.x6.nabble.com/file/n5009051/Sample_image.png>

The image on the right and left essentially the same opened in different
programs.. Would really appreciate if someine can explain to me how to stop
this annoying behaviour!



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[dscho]

Hi,

On Wed, 6 Aug 2014, Mr_Sonky wrote:

> Hi all, I've got a simple question. Why does FIJI open my stack of
> grayscale images as a colour image?? I know it does this because of the
> letter "c" in place of the "play" button when we want to scroll between
> slices in a stack.  Also it does this annoying thing where it colour
> codes i.e. Slice #1: Red, Slice #2: Green..etc.. this goes on to Slice
> #6: Yellow.. and Slice 7 onwards to Slice 361 remains gray (its original
> colour). All images are acquired by a monochromatic sensor so I know the
> colour is not real.
>
> When I apply a 'Grays' LUT, it either doesn't save or I wants me to
> convert to 8-bits first. But doing so doesnt solve the problem of the
> "c" slider.  In addition, I found that when the "c" slider is present, I
> can't adjust the Brightness/Contrast for all slices whereas before I
> normally could with a standard greyscale stack. *When I tried opening
> the SAME image file using ImageJ, it opens normally* without the
> pseudo-colouring the first 6 slices.  Everyhting else also works when
> opened in ImageJ (as opposed to FIJI)
>
> <http://imagej.1557.x6.nabble.com/file/n5009051/Sample_image.png>
>
> The image on the right and left essentially the same opened in different
> programs.. Would really appreciate if someine can explain to me how to stop
> this annoying behaviour!

First of all, I understand your frustration. It still would be a good idea
to be a little gentler if you want somebody else to fix the problem for
you.

Further, as John pointed out, this might be caused by SCIFIO reading
images now. Remember, we are in the process of future-proofing ImageJ and
part of that is to switch to a new image file input/output layer: SCIFIO.

The best way to make sure that your grayscale images are read correctly is
to be friendly to the people who you ask to work for you, free of cost,
and follow the excellent instructions provided here:
http://imagej.net/Bug_reporting_best_practices

In particular, I'd like to point out the second bullet point here:
"Provide a minimal, complete, verifiable example." This is crucial. In
other words, write out a *minimal* grayscale stack that you expected to be
read back as grayscale, and then attach it to the bug report.

Hopefully this helps,
Johannes

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[Mark Hiner-2]

Hi all,

>I encounter an issue that FIJI (ImageJ2) did not open my RGB image
correctly but it works again after I turn off SCIFO.

I just wanted to add that this recommendation is also in the bug reporting
best practices
<http://imagej.net/Bug_reporting_best_practices#Disable_SCIFIO>, with the
caveat that disabling SCIFIO is a temporary workaround. These bugs should
still be reported, as they will need to be resolved eventually.

On Thu, Aug 7, 2014 at 4:10 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi,
>
> On Wed, 6 Aug 2014, Mr_Sonky wrote:
>
> > Hi all, I've got a simple question. Why does FIJI open my stack of
> > grayscale images as a colour image?? I know it does this because of the
> > letter "c" in place of the "play" button when we want to scroll between
> > slices in a stack.  Also it does this annoying thing where it colour
> > codes i.e. Slice #1: Red, Slice #2: Green..etc.. this goes on to Slice
> > #6: Yellow.. and Slice 7 onwards to Slice 361 remains gray (its original
> > colour). All images are acquired by a monochromatic sensor so I know the
> > colour is not real.
> >
> > When I apply a 'Grays' LUT, it either doesn't save or I wants me to
> > convert to 8-bits first. But doing so doesnt solve the problem of the
> > "c" slider.  In addition, I found that when the "c" slider is present, I
> > can't adjust the Brightness/Contrast for all slices whereas before I
> > normally could with a standard greyscale stack. *When I tried opening
> > the SAME image file using ImageJ, it opens normally* without the
> > pseudo-colouring the first 6 slices.  Everyhting else also works when
> > opened in ImageJ (as opposed to FIJI)
> >
> > <http://imagej.1557.x6.nabble.com/file/n5009051/Sample_image.png>
> >
> > The image on the right and left essentially the same opened in different
> > programs.. Would really appreciate if someine can explain to me how to
> stop
> > this annoying behaviour!
>
> First of all, I understand your frustration. It still would be a good idea
> to be a little gentler if you want somebody else to fix the problem for
> you.
>
> Further, as John pointed out, this might be caused by SCIFIO reading
> images now. Remember, we are in the process of future-proofing ImageJ and
> part of that is to switch to a new image file input/output layer: SCIFIO.
>
> The best way to make sure that your grayscale images are read correctly is
> to be friendly to the people who you ask to work for you, free of cost,
> and follow the excellent instructions provided here:
> http://imagej.net/Bug_reporting_best_practices
>
> In particular, I'd like to point out the second bullet point here:
> "Provide a minimal, complete, verifiable example." This is crucial. In
> other words, write out a *minimal* grayscale stack that you expected to be
> read back as grayscale, and then attach it to the bug report.
>
> Hopefully this helps,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Mr_Sonky]

Hi all,

 From LIM Soon Yew John (IMB),"Are you using FIJI (ImageJ2)? If yes, you can try to turn off the SCIFIO under Edit>Options>ImageJ2. I encounter an issue that FIJI (ImageJ2) did not open my RGB image correctly but it works again after I turn off SCIFO. Another thing that you can try is go to Image>Hyperstacks>Stack to Hyperstack..., set the correct number of slices and channel."

firstly, thank you John, I had not realised that SCIFIO opening the files was the problem. Your solution worked right off the bat  Actually, the first thing I tried was turning it into a hyperstack and specifying the colour but that did not work.

From Mark Hiner-2,"I just wanted to add that this recommendation is also in the bug reporting best practices <http://imagej.net/Bug_reporting_best_practices#Disable_SCIFIO>, with the
caveat that disabling SCIFIO is a temporary workaround. These bugs should
still be reported, as they will need to be resolved eventually."

Yes Mark, I have read that turning off SCIFIO was the first troubleshooting step. I now realised that I have stumbled upon a "bug" whereas previously I thought the problem was myself - I simply thought I was doing something wrong and choosing the wrong options in FIJI. I was annoyed more at myself rather than at the program.

From dscho ,"The best way to make sure that your grayscale images are read correctly is
to be friendly to the people who you ask to work for you, free of cost, and follow the excellent instructions provided here: http://imagej.net/Bug_reporting_best_practices" 

I am really sorry I have offended where I genuinely wanted to seek help. I will in the future avoid expressing disappointment and not use words like "annoying". I have left my original post unedited as an example of how not to approach for help in a public forum. As I said, I did not realise that I have stumbled upon a bug. I will report it via FIJI>Help>Report a Bug as soon as I can. Thank you for referring the above mentioned guides .