Problem stitching microscopic images  

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treinisch
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Problem stitching microscopic images

by treinisch » Thu May 30, 2013 1:17 pm

Hallo,

I m trying to stitch some (around 100) images taken using a microscope,
I ve set focal length to 250 mm and I tried many variations for recognition and optimization
(hope these are the right terms, my user interface is in german)

Creating a panorama fails totally.

One thing that I figured out is that lens correction must be disabled which seems somewhat logical.

One problem that I identified is that there a many false links, while important correct links are missing, I
think the main reason is the extreme similarity of the structures.

Any hints?

I have attached one of the images with reduced size as an example and if you want you can download
the complete set here: http://drsvanhay.de/fertig.zip (Attention: 660 MB)


Kind regards

Timm

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Pipetman
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by Pipetman » Thu May 30, 2013 2:47 pm

I'm not an expert in Autopano, but I have some experience with microscopic images (although not so much with stitching them).

I assume, you don't have a motorized stage. These usually have nanometer precision, which allows you to just assemble a montage from individual images (no stitching needed). In this case you can just run e.g. a simple ImageMagick script to put them together; most microscope software should also be able to do this. You need good flat field correction, though, to avoid seams showing between the images.

You mentioned that your images contain very similar structures and that probably makes it very hard for the autodetect algorithm to put them in the right order (I deal a lot with images from cultured cells and these would certainly be impossible for autodetect to put in the right order), so you probably have to manually re-arrange them (see the help function or other threads here for how to do this). Then you might also have to go into the control point editor and manually set control points in the right spots.

By setting the focal length to 250mm you forced mosaic mode already (sorry, borrowing Hugin language here - not sure, if there is an Autopano equivalent), but it might(?) help to also set yaw, pitch and roll to 0.
Last edited by Pipetman on Thu May 30, 2013 3:02 pm, edited 1 time in total.

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treinisch
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by treinisch » Thu May 30, 2013 6:38 pm

Hallo,

Pipetman wrote:I'm not an expert in Autopano, but I have some experience with microscopic images (although not so much with stitching them).

You mentioned that your images contain very similar structures and that probably makes it very hard for the autodetect algorithm to put them in the right order (I deal a lot with images from cultured cells and these would certainly be impossible for autodetect to put in the right order), so you probably have to manually re-arrange them (see the help function or other threads here for how to do this). Then you might also have to go into the control point editor and manually set control points in the right spots.

solved! Creating control-points half automatic is easy, fast and works very well.

thanks

Timm
Last edited by treinisch on Thu May 30, 2013 7:06 pm, edited 1 time in total.

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by geko5766 » Thu May 30, 2013 7:21 pm

Hello,

ty this pano.file.

Focal length manual to 1000mm
Quality of recognition high
Optimization for gigapixel

Should work

Best
Georg

pls rename to .pano
Last edited by geko5766 on Thu May 30, 2013 7:25 pm, edited 1 time in total.
The picture is made behind the camera.......

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by geko5766 » Thu May 30, 2013 7:38 pm

Hello,

ty this pano.file.

Focal length manual to 1000mm
Quality of recognition high
Optimization for gigapixel

Should work

Best
Georg
The picture is made behind the camera.......


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