creating metadata file for tiffs to be loaded into BigStitcher

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creating metadata file for tiffs to be loaded into BigStitcher

MChapman
Hello all,

I have been periodically trying to get BigStitcher to work for my larger
mosaics, but I am having a heck of a time getting the metadata file figured
out for the file import.

I currently rely heavily on the Grid/Collection Stitching plugin which has
the option to input the grid dimensions, overlap, and file name information
and I am trying figure out how to create the necessary metadata files from
the same information.

Any direction on this would be greatly appreciated.
Mike



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Re: creating metadata file for tiffs to be loaded into BigStitcher

Yuekan Jiao-2
Hi

I had the same issue with BigStitcher and am still relying on
Grid/Collection stitching and MIST. I am mainly interested in stitching
larger mosaics (as it was said for BigStitcher), can it actually stitch
mosaics > 2GB?

Yuekan

On Thu, Feb 8, 2018 at 12:46 PM, MChapman <[hidden email]> wrote:

> Hello all,
>
> I have been periodically trying to get BigStitcher to work for my larger
> mosaics, but I am having a heck of a time getting the metadata file figured
> out for the file import.
>
> I currently rely heavily on the Grid/Collection Stitching plugin which has
> the option to input the grid dimensions, overlap, and file name information
> and I am trying figure out how to create the necessary metadata files from
> the same information.
>
> Any direction on this would be greatly appreciated.
> Mike
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: creating metadata file for tiffs to be loaded into BigStitcher

Stephan.Preibisch@mdc-berlin.de
Hi,

I hope I can help. What do you mean by "getting the metadata file figured out for the file import”? It sounds like you attempt to write the XML yourself? The idea is to never touch the actual XML, this is done by the code and basically an internal format. The general (macro-scriptable via BigStitcher > Batch Processing) workflow is:

1) BigStitcher > BigStitcher
2) Define New Dataset
3) Select AutoLoader
4) Select all files of your acquisition (e.g. /home/preibisch/acq/*.tif - or wherever all your files are)
5) Confirm Identified File Patterns (what in the filenames or within each file is a Tile, Channel, …), Calibration, and how to move them to an approximate position (usually select interactive except the metadata contains their positions)
6) Optionally: Resave as HDF5 (highly suggested for large acquisitions), but for sure use virtual loading
7) Interactively Move them to the right location based on (if you only use virtual loading try not to rotate out of plane by accident)
8) Right click > Stitch Dataset and follow the GUI
9) Optionally: Right click > Refine with ICP
9) Right click > Fuse and follow the GUI

We try to explain things on the Wiki: http://imagej.net/BigStitcher

Does this help? Please let me know where you get stuck or what the problem is.

All the best,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
Building 89, 1.08b
Robert-Rössle-Str. 10
13125 Berlin

email: [hidden email]<mailto:[hidden email]>
web: http://preibischlab.mdc-berlin.de
twitter: http://twitter.com/preibischs

On Feb 9, 2018, at 2:29 AM, Yuekan Jiao <[hidden email]<mailto:[hidden email]>> wrote:

Hi

I had the same issue with BigStitcher and am still relying on
Grid/Collection stitching and MIST. I am mainly interested in stitching
larger mosaics (as it was said for BigStitcher), can it actually stitch
mosaics > 2GB?

Yuekan

On Thu, Feb 8, 2018 at 12:46 PM, MChapman <[hidden email]<mailto:[hidden email]>> wrote:

Hello all,

I have been periodically trying to get BigStitcher to work for my larger
mosaics, but I am having a heck of a time getting the metadata file figured
out for the file import.

I currently rely heavily on the Grid/Collection Stitching plugin which has
the option to input the grid dimensions, overlap, and file name information
and I am trying figure out how to create the necessary metadata files from
the same information.

Any direction on this would be greatly appreciated.
Mike



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Re: creating metadata file for tiffs to be loaded into BigStitcher

MChapman
Stephan,

Thanks for the reply, and I have been trying to work through the wiki page
periodically over the past few months.

My first hang-up was in Step 3 - Select Autoloader.  I thought that the "XML
filename" region meant that it wanted an XML file in the folder that I was
going to point to, but now I realize that may be where it is going to write
the xml file.

Since I have now gotten into actually loading the images, I will play a bit
more and come back with more questions.

Thanks!
Mike



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Re: creating metadata file for tiffs to be loaded into BigStitcher

Stephan.Preibisch@mdc-berlin.de
Hi, thanks for the input. I just adjusted the Dialog to be hopefully be more intuitive. Will make a new release soon.

All the best,
Stephan

---

Dr. Stephan Preibisch
Group Leader

Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
Building 89, 1.08b
Robert-Rössle-Str. 10
13125 Berlin

email: [hidden email]<mailto:[hidden email]>
web: http://preibischlab.mdc-berlin.de
twitter: http://twitter.com/preibischs

[cid:5A7E9874-4668-46EB-8060-06B40D9E5849]
On Feb 9, 2018, at 10:20 PM, MChapman <[hidden email]<mailto:[hidden email]>> wrote:

Stephan,

Thanks for the reply, and I have been trying to work through the wiki page
periodically over the past few months.

My first hang-up was in Step 3 - Select Autoloader.  I thought that the "XML
filename" region meant that it wanted an XML file in the folder that I was
going to point to, but now I realize that may be where it is going to write
the xml file.

Since I have now gotten into actually loading the images, I will play a bit
more and come back with more questions.

Thanks!
Mike



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