Posted by
ctrueden on
URL: http://imagej.273.s1.nabble.com/counting-cells-tp5001091p5001818.html
Hi Thuraya,
> while um doing the order "fill holes" this is the image i got
I was able to essentially duplicate your (erroneous) result by first
running the "Invert LUT" command before running Fill Holes. So it seems the
Fill Holes command is sensitive to the LUT somehow.
Is your Fiji fully up to date? (Help > Update Fiji)
When I run the "Create Mask" command with a fully up to date Fiji on OS X,
I receive a Mask window with "8-bit (inverting LUT)" in the title area. I
notice in your screenshot that your LUT is not inverted like that. So I
suspect your error has something to do with the LUT. Are you inverting it
manually? Or do you have the "Use inverting lookup table" option in Edit >
Options > Appearance checked? (That option is off for me.)
If you are stumped, you can probably avoid the issue by running "Invert
LUT" followed by "Fill Holes" followed by "Invert LUT" again. Though
ideally it would be best to learn why the problem is happening, of course.
Regards,
Curtis
P.S. Note that it is also possible for the "Fill Holes" command to behave
unexpectedly if you have many dense particles that are all connected in a
large structure. The command interprets it as one giant structure which
needs filling in. So if you used a substantially wider Brightness setting
than 0-180 with your image, you may experience this phenomenon as well. In
short, try to get your particles well-separated when possible.
On Wed, Feb 20, 2013 at 12:06 PM, Thuraya Medhat
<
[hidden email]>wrote:
> >
> > it's me again um realy sorry for bothering but while um doing the order''
> > fill holes'' this is the image i got idunnu wt's gone wrong
> >
>
>
> >
http://img10.imageshack.us/img10/3083/14615797.png> >
>
>
> >
> > On Mon, Dec 10, 2012 at 11:50 PM, Curtis Rueden <
[hidden email]>
> wrote:
> >
> >> Hi Thuraya,
> >>
> >> > could you please do a screen shot about what you mean when you said
> >> > "- Click the Select button in the Threshold Color dialog to create a
> >> > selection''
> >>
> >> Look again at the screenshot I already linked:
> >>
> >>
http://code.imagej.net/curtis/fiji-particles.jpg> >>
> >> You see the dialog box entitled "Threshold Color"? There is a button at
> >> the
> >> bottom called "Select", which is what I was referring to. This button
> >> creates a selection based on the defined threshold, which you can then
> >> convert to a mask, etc.
> >>
> >> -Curtis
> >>
> >>
> >> On Mon, Dec 10, 2012 at 2:56 PM, Thuraya Medhat <
>
[hidden email]
> >> >wrote:
> >>
> >> > Dear curties,
> >> > you realy did a WONDERFUL job,, just need one thing you told me to do
> >> > selection before i do the mask option
> >> > but that doesn't work with me could you please do a screen shot about
> >> what
> >> > you mean when you said "- Click the Select button in the Threshold
> Color
> >> > dialog to create a selection''
> >> >
> >> > On Mon, Dec 10, 2012 at 8:41 PM, Curtis Rueden <
[hidden email]>
> >> wrote:
> >> >
> >> > > - Click the Select button in the Threshold Color dialog to create a
> >> > > selection
> >> > >
> >> >
> >> > --
> >> > 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