http://imagej.273.s1.nabble.com/stitching-with-mask-transparency-non-rectangular-images-tp5004614p5004621.html
Thanks a lot for your explanation and pointer. I'll try that way.
> Hi Adrian,
>
> yes, you can do that with TrakEM2 and some scripting. TrakEM2 enables
> to assign a byte alpha mask to every image in a project and the
> alignment routines work with the alpha-masked images. Blending is
> another story but as you learn how to deal with alpha masks, you may
> just use that for blending later.
>
> Check this Javascript which assigns a rectangular mask to every image
> tile in a TrakEM2 project:
>
>
https://github.com/axtimwalde/fiji-scripts/blob/master/TrakEM2/mask_dat_border.js>
> instead of a rectangular Roi, you would make an OvalRoi.
>
> You can also paint the alpha mask manually into the images by selecting
> an arbitrary Roi on top of the canvas and filling it with
> black/white/grey respectively---that's for the selective dirt parts.
>
> Good luck,
> Stephan
>
>
>
> On Fri, 2013-08-30 at 12:58 +0200, Adrian Daerr wrote:
>> Hello,
>>
>> I have images where only a circular central region shows my sample, the
>> corners of my camera's sensor are not illuminated. I would like to
>> stitch several of these images together, but using only the central part
>> (both for the registration - which is otherwise dominated by the black
>> circular border which is not part of the sample - and for blending
>> obviously). Is this possible in ImageJ ? Is there a stitching plugin
>> which accepts either a ROI selection, or a binary mask image, selecting
>> the parts of the images to take into account ?
>>
>> I could of course inscribe a rectangle in the circular aperture and crop
>> to it, but I wouldn't have sufficient overlap any more in the pictures I
>> have taken so far (of course in the future I could just take about four
>> times as many pictures to get a denser coverage). And the cropping
>> solution would not be applicable in another case where I'd very much
>> like to be able to exclude some regions from the stitching: when there
>> is a bit of dirt or another defect at a fixed position with respect to
>> the sensor, covering a spot in one image which is nicely visible in
>> another shifted view. Currently the stitched image will blend the dirt
>> with the undamaged spot.
>>
>> The hugin/enblend software suite has the possibility to define 'include'
>> and 'exclude' regions, but if I could avoid the detour and do the stuff
>> in Fiji that would be splendid.
>>
>> Thanks in advance,
>> Adrian
>>
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