browse image set in x, y, and time

[Lars Damgaard]

I study bacteria on slides and want to be able to both search the area for interesting details but may also choose to see  the big picture as a function of time. In other words, some kind of movie experience which is interactive in terms of both movie speed, zoom and ROI location. Does such a thing exist?

My current approach is:
I produce sets of highly-resolved images (e.g. 6 rows by 15 columns) with our motorized microscope system (Zeiss Observer Z1) to cover a sufficiently large area and I repeat this at a given time interval. Each set is saved in a separate folder within a folder for the entire experiment.

To view the result, I have found the following (un-satisfying) approaches:
I stitch each set to a large image, then I either
1) open the first of the large images in a general image viewer (e.g. Windows Photo Viewer) , and make the 'movie' experience of the big picture by browsing through the files with the arrow/pagedown button. I can also zoom in on details in a single image, but when I select the next picture, the viewer un-zooms, so I need to re-zoom and definitely don't get a 'movie experience'.
 - or -
2) In the general image viewer, try to decide for a special ROI. All the large images are then imported as an Image Sequence in ImageJ, where I crop the sequence to the ROI and save the sequence (Save As) .avi. Playing the resulting file gives me a nice 'movie experience' of the ROI, but if I find that I want another ROI, I need to do 2) over again - not very fast or interactive.

So as an satisfying alternative I imagine a window where I can zoom in on any ROI and then press Play to see the ROI as a movie (and pause, reverse, change speed). I could press the arrows keys to shift ROI vertically or horizontally, and I could zoom in and out - both on the fly as the sequence is played. Does such a thing exist?
I think the most computer efficient approach may be to NOT stitch the single images, but rather only load those involved in the actual ROI at any time, simply placing them according to their coordinates. Stitching with advanced calculations of the overlaps should is not necessary.
Can anyone suggest a way to go?

Best regards, Lars

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[Mario Faretta-2]

Hi Lars,
just a trick not the solution you required:
instead of cropping, duplicate the entire stack (if a ROI is active, the
new stack will contain only the content of the ROI). Obviously at some
time you will have to close some windows to avoid memory crash.
Hope it helps
Mario

On 08/01/2013 14:50, Lars Damgaard wrote:

> I study bacteria on slides and want to be able to both search the area for interesting details but may also choose to see  the big picture as a function of time. In other words, some kind of movie experience which is interactive in terms of both movie speed, zoom and ROI location. Does such a thing exist?
>
> My current approach is:
> I produce sets of highly-resolved images (e.g. 6 rows by 15 columns) with our motorized microscope system (Zeiss Observer Z1) to cover a sufficiently large area and I repeat this at a given time interval. Each set is saved in a separate folder within a folder for the entire experiment.
>
> To view the result, I have found the following (un-satisfying) approaches:
> I stitch each set to a large image, then I either
> 1) open the first of the large images in a general image viewer (e.g. Windows Photo Viewer) , and make the 'movie' experience of the big picture by browsing through the files with the arrow/pagedown button. I can also zoom in on details in a single image, but when I select the next picture, the viewer un-zooms, so I need to re-zoom and definitely don't get a 'movie experience'.
>   - or -
> 2) In the general image viewer, try to decide for a special ROI. All the large images are then imported as an Image Sequence in ImageJ, where I crop the sequence to the ROI and save the sequence (Save As) .avi. Playing the resulting file gives me a nice 'movie experience' of the ROI, but if I find that I want another ROI, I need to do 2) over again - not very fast or interactive.
>
> So as an satisfying alternative I imagine a window where I can zoom in on any ROI and then press Play to see the ROI as a movie (and pause, reverse, change speed). I could press the arrows keys to shift ROI vertically or horizontally, and I could zoom in and out - both on the fly as the sequence is played. Does such a thing exist?
> I think the most computer efficient approach may be to NOT stitch the single images, but rather only load those involved in the actual ROI at any time, simply placing them according to their coordinates. Stitching with advanced calculations of the overlaps should is not necessary.
> Can anyone suggest a way to go?
>
> Best regards, Lars
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Joel Sheffield]

I'm a little puzzled.  Can you import each of the stitched images to form a
stack in ImageJ and then use the "animate stack" to view the "movie"?  You
could also use the magnification functon to enlarge a specific area.  Or,
are the stitched images too large to do this with?  What are the pixel
dimensions of the stitched image, and how many do you have?

Joel


Joel

On Tue, Jan 8, 2013 at 9:10 AM, Mario Faretta <[hidden email]> wrote:

> Hi Lars,
> just a trick not the solution you required:
> instead of cropping, duplicate the entire stack (if a ROI is active, the
> new stack will contain only the content of the ROI). Obviously at some time
> you will have to close some windows to avoid memory crash.
> Hope it helps
> Mario
>
>
> On 08/01/2013 14:50, Lars Damgaard wrote:
>
>> I study bacteria on slides and want to be able to both search the area
>> for interesting details but may also choose to see  the big picture as a
>> function of time. In other words, some kind of movie experience which is
>> interactive in terms of both movie speed, zoom and ROI location. Does such
>> a thing exist?
>>
>> My current approach is:
>> I produce sets of highly-resolved images (e.g. 6 rows by 15 columns) with
>> our motorized microscope system (Zeiss Observer Z1) to cover a sufficiently
>> large area and I repeat this at a given time interval. Each set is saved in
>> a separate folder within a folder for the entire experiment.
>>
>> To view the result, I have found the following (un-satisfying) approaches:
>> I stitch each set to a large image, then I either
>> 1) open the first of the large images in a general image viewer (e.g.
>> Windows Photo Viewer) , and make the 'movie' experience of the big picture
>> by browsing through the files with the arrow/pagedown button. I can also
>> zoom in on details in a single image, but when I select the next picture,
>> the viewer un-zooms, so I need to re-zoom and definitely don't get a 'movie
>> experience'.
>>   - or -
>> 2) In the general image viewer, try to decide for a special ROI. All the
>> large images are then imported as an Image Sequence in ImageJ, where I crop
>> the sequence to the ROI and save the sequence (Save As) .avi. Playing the
>> resulting file gives me a nice 'movie experience' of the ROI, but if I find
>> that I want another ROI, I need to do 2) over again - not very fast or
>> interactive.
>>
>> So as an satisfying alternative I imagine a window where I can zoom in on
>> any ROI and then press Play to see the ROI as a movie (and pause, reverse,
>> change speed). I could press the arrows keys to shift ROI vertically or
>> horizontally, and I could zoom in and out - both on the fly as the sequence
>> is played. Does such a thing exist?
>> I think the most computer efficient approach may be to NOT stitch the
>> single images, but rather only load those involved in the actual ROI at any
>> time, simply placing them according to their coordinates. Stitching with
>> advanced calculations of the overlaps should is not necessary.
>> Can anyone suggest a way to go?
>>
>> Best regards, Lars
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

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[Lars Damgaard]

Hi Joel,

My stitched pictures are 6947 x 11869 pixels 24 bit color and are made up of 6 x 18 individual images of 1388 x 1038.
ImageJ can do the zoom as you propose, but very slowly with such big images. And also, I couldn't find out how to move up and down once zoomed, and finally I don't think it could run by itself without med clicking on the next picture arrow.

Lars

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