[OpenSPIM] Multiview registration - no inliers

[Tania Mendonca]

Hi

Just tried it but it still doesn't work.

Thanks
Tania

On 19 August 2016 at 20:13, Stephan.Preibisch at mdc-berlin.de <
Stephan.Preibisch at mdc-berlin.de> wrote:

> 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>
> 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 <
> 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>
>> 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
>> --
>> -------------------------
>> Tania Mendonca
>> Doctoral Research Student
>> University of Sheffield
>> S10 2TN
>> -------------------------
>>
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>>
>>
>
>
> --
> -------------------------
> Tania Mendonca
> Doctoral Research Student
> University of Sheffield
> S10 2TN
> -------------------------
>
>


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