[ome-users] FlowSight .cif file opened with low resolution

[Minh Doan]

Hello Melissa,

Many thanks for your return.

As requested, here are the screenshot I took of the
export_to_cif_for_later_tiff.cif being opened in IDEAS.

Also, one of my senior colleagues have just had an independent
investigation. And he theorized that, maybe the display by IDEAS is a
"smoothed" display. Please see the discussion below:

----
I've been digging a lot deeper into to this and now I'm even more convinced
that the tiffs we get from bioformats is the raw data that the Imagestream
machine actually records (it isn't a conventional microscope and the
resolution is between 0.33 and 0.5um so typical 10um cells would have a
width of 20-30 pixels) - in IDEAS a lot of data massage goes on - e.g. if
you load an image into the workspace and zoom it constantly smooths the
image for presentation

the other thing that convinces me of this is that if you load an image in
IDEAS and use 'Draw line profile' to draw a line across the width of the
cell it gives the length of the line in pixels (not fractions of pixels)
and this corresponds exactly to the width of the cell you get from the
tiffs generated by bioformats

in the creat tiffs module you can clearly output data in the raw format
(for analysis) but maybe even this is being modified ???

----

We could not confirm this theory at the moment, because similar to you, we
do not have an access to FlowSight/Amnis data structure, we only have an
installed IDEAS version 6.0 in Windows.

Hope that helps.
Many thanks again.

On Wed, Jan 18, 2017 at 12:32 PM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:

> Hi Minh,
>
> Thank you for reporting this problem.
>
> > I'm working on a project that uses Amnis FlowSight .cif , which could be
> opened by Bioformats (MATLAB version and python-bioformats)
> >
> > Unfortunately the resolution of the image after being opened by both of
> the versions are lossy. Can anyone so kind to help me check this out.
>
> I can confirm that Bio-Formats reports images that are approximately
> 35x35 to 55x55 pixels for the attached
> export_to_cif_for_later_tiff.cif.  However, I so far have not been
> able to find evidence of higher resolution images in the file.
>
> > I send here 2 screenshots, one that compares between image opened by
> python-bioformats and its original form (export directly from Amnis IDEAS).
> And the other screenshot compare image opened by MATLAB-bioformats package,
> > compared with its original form
> >
> > I also attach an example .cif file.
>
> From the screenshots, it looks like export_to_cif_for_later_tiff.cif
> is not the file being opened in IDEAS or MATLAB.  Could you please
> confirm that the screenshots do indeed represent a different file?  If
> so, could you please send a relevant screenshot of
> export_to_cif_for_later_tiff.cif being opened/exported in IDEAS?  In
> either case, do you have an idea of what the correct X and Y
> dimensions should be?  The OME team does not have access to the Amnis
> IDEAS software, so any additional information you can provide would be
> very helpful for debugging.
>
> Regards,
> -Melissa
>
> On Tue, Jan 17, 2017 at 2:40 PM, Minh Doan <minhdoan at broadinstitute.org>
> wrote:
> > Hello all, good afternoon,
> >
> > I am Minh Doan, a postdoc in imaging platform of Broad Institute. I'm
> > working on a project that uses Amnis FlowSight .cif , which could be
> opened
> > by Bioformats (MATLAB version and python-bioformats)
> >
> > Unfortunately the resolution of the image after being opened by both of
> the
> > versions are lossy. Can anyone so kind to help me check this out.
> >
> > I send here 2 screenshots, one that compares between image opened by
> > python-bioformats and its original form (export directly from Amnis
> IDEAS).
> > And the other screenshot compare image opened by MATLAB-bioformats
> package,
> > compared with its original form
> >
> > I also attach an example .cif file.
> >
> > Any advices are very much appreciated.
> >
> > Bests,
> > Minh
> >
> > --
> >
> > Minh Doan, M.D., Ph.D.
> > Imaging Platform
> > Broad Institute of Harvard and MIT
> > 415 Main Street,
> > Cambridge MA 02142
> > phone: (617) 714-7681
> > minhdoan at broadinstitute.org
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
>



-- 

Minh Doan, M.D., Ph.D.
Imaging Platform
Broad Institute of Harvard and MIT
415 Main Street,
Cambridge MA 02142
phone: (617) 714-7681
minhdoan at broadinstitute.org <nathalie.court at pasteur.fr>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170118/1412b275/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Channel_1_not_zoomed.PNG
Type: image/png
Size: 588679 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170118/1412b275/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Channel_7_not_zoomed.PNG
Type: image/png
Size: 456145 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170118/1412b275/attachment-0005.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Channel_7_zoomed.PNG
Type: image/png
Size: 440161 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170118/1412b275/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Channel_1_zoomed.PNG
Type: image/png
Size: 608041 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170118/1412b275/attachment-0007.png>