Image5D bug?

[Jacob Keller-2]

I have been using the nice capabilities of image5D, but there seem to be a
couple of problems. My procedure is to split multichannel .czi xyzct stacks
into individual channels, stack-to-image5D, then montage. I noticed some
strange behaviors in so doing:

-when I make a montage, it is output as RGB, even though the input is 8- or
16-bit. Not too terrible, since it's easy enough to convert to 8-bit from
there, although it's a shame to lose the 16-bit depth, and it seems like
something funky is going on.

-the last frame in the timelapse montages are always black

-Contrast is weird: when I do not click "copy contrast" the images are
output way too bright, and it's not just the contrast setting. When I do
click "copy contrast," sometimes things are fine, sometimes the intensities
(not just contrast settings) make discrete jumps inexplicably.

Can you help me out here?

Jacob Keller

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

[ctrueden]

Hi Jacob,

The Image5D plugin, while currently part of Fiji, is not actively supported
[1].

Is there some reason that ImageJ's built-in support for 5D hyperstacks,
along with the "Make Montage..." command, cannot accomplish what you need?

The following macro creates a 16-bit montage of two images without using
Image5D:

run("Blobs (25K)");
run("16-bit");
run("Clown (14K)");
run("16-bit");
run("Images to Stack", "method=[Copy (center)] name=Stack title=[] use");
run("Make Montage...", "columns=2 rows=1 scale=1");

Regards,
Curtis

[1] http://imagej.net/Image5D; see right-hand sidebar

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Aug 23, 2017 at 6:05 PM, Jacob Keller <[hidden email]>
wrote:

> I have been using the nice capabilities of image5D, but there seem to be a
> couple of problems. My procedure is to split multichannel .czi xyzct stacks
> into individual channels, stack-to-image5D, then montage. I noticed some
> strange behaviors in so doing:
>
> -when I make a montage, it is output as RGB, even though the input is 8- or
> 16-bit. Not too terrible, since it's easy enough to convert to 8-bit from
> there, although it's a shame to lose the 16-bit depth, and it seems like
> something funky is going on.
>
> -the last frame in the timelapse montages are always black
>
> -Contrast is weird: when I do not click "copy contrast" the images are
> output way too bright, and it's not just the contrast setting. When I do
> click "copy contrast," sometimes things are fine, sometimes the intensities
> (not just contrast settings) make discrete jumps inexplicably.
>
> Can you help me out here?
>
> Jacob Keller
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Jacob Keller-2]

I get the error msg "5D hyperstacks are not supported." Pls find attached
MCVE (same as other post.) This also happens when I get rid of one channel,
so it's only 4D.

Jacob

On Thu, Aug 24, 2017 at 10:49 AM, Curtis Rueden <[hidden email]> wrote:

> Hi Jacob,
>
> The Image5D plugin, while currently part of Fiji, is not actively supported
> [1].
>
> Is there some reason that ImageJ's built-in support for 5D hyperstacks,
> along with the "Make Montage..." command, cannot accomplish what you need?
>
> The following macro creates a 16-bit montage of two images without using
> Image5D:
>
> run("Blobs (25K)");
> run("16-bit");
> run("Clown (14K)");
> run("16-bit");
> run("Images to Stack", "method=[Copy (center)] name=Stack title=[] use");
> run("Make Montage...", "columns=2 rows=1 scale=1");
>
> Regards,
> Curtis
>
> [1] http://imagej.net/Image5D; see right-hand sidebar
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Aug 23, 2017 at 6:05 PM, Jacob Keller <[hidden email]>
> wrote:
>
> > I have been using the nice capabilities of image5D, but there seem to be
> a
> > couple of problems. My procedure is to split multichannel .czi xyzct
> stacks
> > into individual channels, stack-to-image5D, then montage. I noticed some
> > strange behaviors in so doing:
> >
> > -when I make a montage, it is output as RGB, even though the input is 8-
> or
> > 16-bit. Not too terrible, since it's easy enough to convert to 8-bit from
> > there, although it's a shame to lose the 16-bit depth, and it seems like
> > something funky is going on.
> >
> > -the last frame in the timelapse montages are always black
> >
> > -Contrast is weird: when I do not click "copy contrast" the images are
> > output way too bright, and it's not just the contrast setting. When I do
> > click "copy contrast," sometimes things are fine, sometimes the
> intensities
> > (not just contrast settings) make discrete jumps inexplicably.
> >
> > Can you help me out here?
> >
> > Jacob Keller
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[ctrueden]

Hi Jacob,

> I get the error msg "5D hyperstacks are not supported."

It will work if you use the "Image > Hyperstacks > Hyperstack to Stack"
command first.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Aug 24, 2017 at 10:32 AM, Jacob Keller <[hidden email]>
wrote:

> I get the error msg "5D hyperstacks are not supported." Pls find attached
> MCVE (same as other post.) This also happens when I get rid of one channel,
> so it's only 4D.
>
> Jacob
>
> On Thu, Aug 24, 2017 at 10:49 AM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Jacob,
> >
> > The Image5D plugin, while currently part of Fiji, is not actively
> supported
> > [1].
> >
> > Is there some reason that ImageJ's built-in support for 5D hyperstacks,
> > along with the "Make Montage..." command, cannot accomplish what you
> need?
> >
> > The following macro creates a 16-bit montage of two images without using
> > Image5D:
> >
> > run("Blobs (25K)");
> > run("16-bit");
> > run("Clown (14K)");
> > run("16-bit");
> > run("Images to Stack", "method=[Copy (center)] name=Stack title=[] use");
> > run("Make Montage...", "columns=2 rows=1 scale=1");
> >
> > Regards,
> > Curtis
> >
> > [1] http://imagej.net/Image5D; see right-hand sidebar
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Wed, Aug 23, 2017 at 6:05 PM, Jacob Keller <[hidden email]>
> > wrote:
> >
> > > I have been using the nice capabilities of image5D, but there seem to
> be
> > a
> > > couple of problems. My procedure is to split multichannel .czi xyzct
> > stacks
> > > into individual channels, stack-to-image5D, then montage. I noticed
> some
> > > strange behaviors in so doing:
> > >
> > > -when I make a montage, it is output as RGB, even though the input is
> 8-
> > or
> > > 16-bit. Not too terrible, since it's easy enough to convert to 8-bit
> from
> > > there, although it's a shame to lose the 16-bit depth, and it seems
> like
> > > something funky is going on.
> > >
> > > -the last frame in the timelapse montages are always black
> > >
> > > -Contrast is weird: when I do not click "copy contrast" the images are
> > > output way too bright, and it's not just the contrast setting. When I
> do
> > > click "copy contrast," sometimes things are fine, sometimes the
> > intensities
> > > (not just contrast settings) make discrete jumps inexplicably.
> > >
> > > Can you help me out here?
> > >
> > > Jacob Keller
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Jacob Keller-2]

Right, it does work...sort of: it only outputs one time point. What I want
is timelapses of each z-slice all on the same x-y plane, to see
simultaneously what's happening at all z-levels. The normal "make montage"
command apparently only works for one time point, whereas the image5D
command accommodates the time dimension and therefore makes the sort of
movie-montage I want. Is it difficult to upgrade the native command to
allow this?

Jacob

On Thu, Aug 24, 2017 at 11:48 AM, Curtis Rueden <[hidden email]> wrote:

> Hi Jacob,
>
> > I get the error msg "5D hyperstacks are not supported."
>
> It will work if you use the "Image > Hyperstacks > Hyperstack to Stack"
> command first.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Thu, Aug 24, 2017 at 10:32 AM, Jacob Keller <[hidden email]>
> wrote:
>
> > I get the error msg "5D hyperstacks are not supported." Pls find attached
> > MCVE (same as other post.) This also happens when I get rid of one
> channel,
> > so it's only 4D.
> >
> > Jacob
> >
> > On Thu, Aug 24, 2017 at 10:49 AM, Curtis Rueden <[hidden email]>
> wrote:
> >
> > > Hi Jacob,
> > >
> > > The Image5D plugin, while currently part of Fiji, is not actively
> > supported
> > > [1].
> > >
> > > Is there some reason that ImageJ's built-in support for 5D hyperstacks,
> > > along with the "Make Montage..." command, cannot accomplish what you
> > need?
> > >
> > > The following macro creates a 16-bit montage of two images without
> using
> > > Image5D:
> > >
> > > run("Blobs (25K)");
> > > run("16-bit");
> > > run("Clown (14K)");
> > > run("16-bit");
> > > run("Images to Stack", "method=[Copy (center)] name=Stack title=[]
> use");
> > > run("Make Montage...", "columns=2 rows=1 scale=1");
> > >
> > > Regards,
> > > Curtis
> > >
> > > [1] http://imagej.net/Image5D; see right-hand sidebar
> > >
> > > --
> > > Curtis Rueden
> > > LOCI software architect - https://loci.wisc.edu/software
> > > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > > Did you know ImageJ has a forum? http://forum.imagej.net/
> > >
> > >
> > > On Wed, Aug 23, 2017 at 6:05 PM, Jacob Keller <[hidden email]>
> > > wrote:
> > >
> > > > I have been using the nice capabilities of image5D, but there seem to
> > be
> > > a
> > > > couple of problems. My procedure is to split multichannel .czi xyzct
> > > stacks
> > > > into individual channels, stack-to-image5D, then montage. I noticed
> > some
> > > > strange behaviors in so doing:
> > > >
> > > > -when I make a montage, it is output as RGB, even though the input is
> > 8-
> > > or
> > > > 16-bit. Not too terrible, since it's easy enough to convert to 8-bit
> > from
> > > > there, although it's a shame to lose the 16-bit depth, and it seems
> > like
> > > > something funky is going on.
> > > >
> > > > -the last frame in the timelapse montages are always black
> > > >
> > > > -Contrast is weird: when I do not click "copy contrast" the images
> are
> > > > output way too bright, and it's not just the contrast setting. When I
> > do
> > > > click "copy contrast," sometimes things are fine, sometimes the
> > > intensities
> > > > (not just contrast settings) make discrete jumps inexplicably.
> > > >
> > > > Can you help me out here?
> > > >
> > > > Jacob Keller
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > > >
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Jacob Keller-2]

FWIW, here is a horrible macro that makes movie montages, but I can't get
some of the variables to work, so one has to input manually the number of
slices (stupid, but can't figure out how to feed it the variable) and the
number of columns/rows for the montage (reasonable, since this is a matter
of taste--ideally it would be a dialogue box, but...)

If anyone wants to make this better, like fixing the variable thing or
adding a dialog box, please do--I would love to learn how to fix it.

All the best,

Jacob Keller


sourceStack = getTitle();
getDimensions(w, h, channels, slices, frames);
//change "slices" below to the correct number
run("Make Substack...", "slices=1-20 frames=1");
rename("sub1");
//change values below to desired number of columns and rows
run("Make Montage...", "columns=4 rows=5 scale=1");
rename("base");
selectWindow("sub1");
close();
 for (i=2; i<=frames; i++) {
  selectWindow(sourceStack);
//change "slices" below to the correct number
run("Make Substack...", "slices=1-20 frames="+i);
rename("tomontage");
//change values below to desired number of columns and rows
run("Make Montage...", "columns=4 rows=5 scale=1");
rename("next");
run("Concatenate...", "  title=base image1=base image2=next image3=[-- None
--]");
selectWindow("tomontage");
close();
}
selectWindow("base");
rename("montage");


On Thu, Aug 24, 2017 at 2:21 PM, Jacob Keller <[hidden email]>
wrote:

> Right, it does work...sort of: it only outputs one time point. What I want
> is timelapses of each z-slice all on the same x-y plane, to see
> simultaneously what's happening at all z-levels. The normal "make montage"
> command apparently only works for one time point, whereas the image5D
> command accommodates the time dimension and therefore makes the sort of
> movie-montage I want. Is it difficult to upgrade the native command to
> allow this?
>
> Jacob
>
> On Thu, Aug 24, 2017 at 11:48 AM, Curtis Rueden <[hidden email]> wrote:
>
>> Hi Jacob,
>>
>> > I get the error msg "5D hyperstacks are not supported."
>>
>> It will work if you use the "Image > Hyperstacks > Hyperstack to Stack"
>> command first.
>>
>> Regards,
>> Curtis
>>
>> --
>> Curtis Rueden
>> LOCI software architect - https://loci.wisc.edu/software
>> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
>> Did you know ImageJ has a forum? http://forum.imagej.net/
>>
>>
>> On Thu, Aug 24, 2017 at 10:32 AM, Jacob Keller <[hidden email]>
>> wrote:
>>
>> > I get the error msg "5D hyperstacks are not supported." Pls find
>> attached
>> > MCVE (same as other post.) This also happens when I get rid of one
>> channel,
>> > so it's only 4D.
>> >
>> > Jacob
>> >
>> > On Thu, Aug 24, 2017 at 10:49 AM, Curtis Rueden <[hidden email]>
>> wrote:
>> >
>> > > Hi Jacob,
>> > >
>> > > The Image5D plugin, while currently part of Fiji, is not actively
>> > supported
>> > > [1].
>> > >
>> > > Is there some reason that ImageJ's built-in support for 5D
>> hyperstacks,
>> > > along with the "Make Montage..." command, cannot accomplish what you
>> > need?
>> > >
>> > > The following macro creates a 16-bit montage of two images without
>> using
>> > > Image5D:
>> > >
>> > > run("Blobs (25K)");
>> > > run("16-bit");
>> > > run("Clown (14K)");
>> > > run("16-bit");
>> > > run("Images to Stack", "method=[Copy (center)] name=Stack title=[]
>> use");
>> > > run("Make Montage...", "columns=2 rows=1 scale=1");
>> > >
>> > > Regards,
>> > > Curtis
>> > >
>> > > [1] http://imagej.net/Image5D; see right-hand sidebar
>> > >
>> > > --
>> > > Curtis Rueden
>> > > LOCI software architect - https://loci.wisc.edu/software
>> > > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
>> > > Did you know ImageJ has a forum? http://forum.imagej.net/
>> > >
>> > >
>> > > On Wed, Aug 23, 2017 at 6:05 PM, Jacob Keller <[hidden email]
>> >
>> > > wrote:
>> > >
>> > > > I have been using the nice capabilities of image5D, but there seem
>> to
>> > be
>> > > a
>> > > > couple of problems. My procedure is to split multichannel .czi xyzct
>> > > stacks
>> > > > into individual channels, stack-to-image5D, then montage. I noticed
>> > some
>> > > > strange behaviors in so doing:
>> > > >
>> > > > -when I make a montage, it is output as RGB, even though the input
>> is
>> > 8-
>> > > or
>> > > > 16-bit. Not too terrible, since it's easy enough to convert to 8-bit
>> > from
>> > > > there, although it's a shame to lose the 16-bit depth, and it seems
>> > like
>> > > > something funky is going on.
>> > > >
>> > > > -the last frame in the timelapse montages are always black
>> > > >
>> > > > -Contrast is weird: when I do not click "copy contrast" the images
>> are
>> > > > output way too bright, and it's not just the contrast setting. When
>> I
>> > do
>> > > > click "copy contrast," sometimes things are fine, sometimes the
>> > > intensities
>> > > > (not just contrast settings) make discrete jumps inexplicably.
>> > > >
>> > > > Can you help me out here?
>> > > >
>> > > > Jacob Keller
>> > > >
>> > > > --
>> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> > > >
>> > >
>> > > --
>> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> > >
>> >
>> > --
>> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> >
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

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

[Krs5]

Not sure I understand this well but is it possible to use Image > Stacks > Tools > Make Substack...? This allows you to make substacks containing the same z-slice from each time point. It requires that the whole time series is one file.

Best wishes

Kees



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jacob Keller
Sent: 24 August 2017 19:21
To: [hidden email]
Subject: Re: Image5D bug?

Right, it does work...sort of: it only outputs one time point. What I want is timelapses of each z-slice all on the same x-y plane, to see simultaneously what's happening at all z-levels. The normal "make montage"
command apparently only works for one time point, whereas the image5D command accommodates the time dimension and therefore makes the sort of movie-montage I want. Is it difficult to upgrade the native command to allow this?

Jacob

On Thu, Aug 24, 2017 at 11:48 AM, Curtis Rueden <[hidden email]> wrote:

> Hi Jacob,
>
> > I get the error msg "5D hyperstacks are not supported."
>
> It will work if you use the "Image > Hyperstacks > Hyperstack to Stack"
> command first.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
> know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Thu, Aug 24, 2017 at 10:32 AM, Jacob Keller
> <[hidden email]>
> wrote:
>
> > I get the error msg "5D hyperstacks are not supported." Pls find
> > attached MCVE (same as other post.) This also happens when I get rid
> > of one
> channel,
> > so it's only 4D.
> >
> > Jacob
> >
> > On Thu, Aug 24, 2017 at 10:49 AM, Curtis Rueden <[hidden email]>
> wrote:
> >
> > > Hi Jacob,
> > >
> > > The Image5D plugin, while currently part of Fiji, is not actively
> > supported
> > > [1].
> > >
> > > Is there some reason that ImageJ's built-in support for 5D
> > > hyperstacks, along with the "Make Montage..." command, cannot
> > > accomplish what you
> > need?
> > >
> > > The following macro creates a 16-bit montage of two images without
> using
> > > Image5D:
> > >
> > > run("Blobs (25K)");
> > > run("16-bit");
> > > run("Clown (14K)");
> > > run("16-bit");
> > > run("Images to Stack", "method=[Copy (center)] name=Stack title=[]
> use");
> > > run("Make Montage...", "columns=2 rows=1 scale=1");
> > >
> > > Regards,
> > > Curtis
> > >
> > > [1] http://imagej.net/Image5D; see right-hand sidebar
> > >
> > > --
> > > Curtis Rueden
> > > LOCI software architect - https://loci.wisc.edu/software
> > > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did
> > > you know ImageJ has a forum? http://forum.imagej.net/
> > >
> > >
> > > On Wed, Aug 23, 2017 at 6:05 PM, Jacob Keller
> > > <[hidden email]>
> > > wrote:
> > >
> > > > I have been using the nice capabilities of image5D, but there
> > > > seem to
> > be
> > > a
> > > > couple of problems. My procedure is to split multichannel .czi
> > > > xyzct
> > > stacks
> > > > into individual channels, stack-to-image5D, then montage. I
> > > > noticed
> > some
> > > > strange behaviors in so doing:
> > > >
> > > > -when I make a montage, it is output as RGB, even though the
> > > > input is
> > 8-
> > > or
> > > > 16-bit. Not too terrible, since it's easy enough to convert to
> > > > 8-bit
> > from
> > > > there, although it's a shame to lose the 16-bit depth, and it
> > > > seems
> > like
> > > > something funky is going on.
> > > >
> > > > -the last frame in the timelapse montages are always black
> > > >
> > > > -Contrast is weird: when I do not click "copy contrast" the
> > > > images
> are
> > > > output way too bright, and it's not just the contrast setting.
> > > > When I
> > do
> > > > click "copy contrast," sometimes things are fine, sometimes the
> > > intensities
> > > > (not just contrast settings) make discrete jumps inexplicably.
> > > >
> > > > Can you help me out here?
> > > >
> > > > Jacob Keller
> > > >
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > > >
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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