[OpenSPIM] Multiview registration - no inliers

[Stephan.Preibisch at mdc-berlin.de]

Hi, I just think that in the beginning when you define your dataset the pixel sizes were wrong which potentially corrupts the downstream workflow. Try to start from the very beginning, and define a new dataset and manually put in the correct calibration. This might just work ...

All the best,
Stephan

Sent from my iPhone

On Aug 19, 2016, at 21:00, Tania Mendonca <tvmendonca1 at sheffield.ac.uk<mailto:tvmendonca1 at sheffield.ac.uk>> wrote:

Hi

I've just checked to make sure but yes I have corrected the voxel size on the image stacks and there shouldn't be a mistake in that. However, your reply gave me an idea and I did a quick test. I duplicated one of the images and ran the multiview reconstruction plugin for the two duplicates. It worked, so it makes me think that there's nothing wrong with the files themselves and you might be right about the issue being with my voxel depth. I've referred to SVI's Nyquist calculator to workout my step size, is there a recommended step size that people use?

Best wishes
Tania

On 19 August 2016 at 16:58, Stephan.Preibisch at mdc-berlin.de<mailto:Stephan.Preibisch at mdc-berlin.de> <Stephan.Preibisch at mdc-berlin.de<mailto:Stephan.Preibisch at mdc-berlin.de>> wrote:
Hi, my first guess would be that your calibration (pixel size is x,y and z) is wrong ... Can you make sure this is correct when you define your dataset?

All the best,
Stephan

On Aug 19, 2016, at 17:17, Tania Mendonca <tvmendonca1 at sheffield.ac.uk<mailto:tvmendonca1 at sheffield.ac.uk>> wrote:

Hi all

Hope your microscopes are aligned and treating you well! I'm sorry if I've missed this conversation before but I was wondering if any of you have had similar problems as me with trying to get the Fiji multiview reconstruction plugin to like my data.

I've tried a range of microspheres - different colours, different sizes and different concentrations but it never seems to find enough correspondences between views. I've been primarily experimenting with interactively detec​​ting interest points. I've tried the presets as well but with no luck. I've tried to systematically work through various combinations of sigma and threshold but always end up with 0 inliers. Registrations always terminates with the following error: "There are no connected tiles, cannot do an optimization. Quitting."

My home built system doesn't run on µManager and my images are acquired as .cxd files which I convert to .tifs before processing. I'm attaching some of my test data - https://drive.google.com/file/d/0B-he-_wcys_-aUtRZ0pidFhyUlk/view?usp=sharing
the sample here is 1µm yellow-green beads (1:4000 dilution) and 10µm beads (1:50 dilution) with the idea of using the 1µm beads to reconstruct the 10µm beads. I use the same objectives as on the OpenSPIM system (10X for illumination and 20X for detection), magnification on the system is 27.7X. The illumination here is 473nm and detection at 520nm.​​

A log file has been included in the zip file to give you an idea of what I've been trying.

I hope I'm just missing a trick somewhere. Any help would be greatly appreciated!

Best wishes
Tania
--
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Tania Mendonca
Doctoral Research Student
University of Sheffield
S10 2TN
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Tania Mendonca
Doctoral Research Student
University of Sheffield
S10 2TN
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