[OpenSPIM] About metadata and SPIM reconstruction, was Re: OpenSPIM update site

[Johannes Schindelin]

Hi Monika,

[I hope you do not mind that I Cc:ed the mailing list; I believe that 
other OpenSPIM people will be interested/helpful]

On 2015-05-05 16:16, Johannes Schindelin wrote:

> On 2015-05-05 16:13, Monika Pawłowska wrote:
> 
>> Now that I figured out how to use maven I wouldn't mind helping a bit
>> more  with the plugin. For instance I would like to figure out what
>> would it  take to remove this step: http://openspim.org/Pre-processing
>> . Do you have  any idea what these "metadata conflicts" are?
> 
> I do not remember, I just found out recently that we (= the lab I am
> working in) are not writing OME Tiffs at all :-( As far as I can tell,
> this is the class that *should* do it:
> 
> https://github.com/openspim/SPIMAcquisition/blob/master/src/main/java/spim/progacq/OMETIFFHandler.java
> 
> But I have no idea what the metadata conflicts are, and as far as I
> can tell, nobody recorded the conflicts, either. I guess we will just
> have to reproduce them, and I half expect the conflicts to have gone
> away in the meantime, anyway.

There was a bug report yesterday: 
https://github.com/bigdataviewer/SPIM_Registration/issues/41

While it concerned CZI files, I imagine that OME Tiff files might expose 
similar problems. If you stumble over such problems, I would suggest 
doing exactly the same as Mario: report the problem on GitHub. Steffi is 
always busy, of course, as we all are, yet he is always helpful.

Ciao,
Dscho