BigStitcher import tile positions as 'Filename defined ' or 'from file'

stitching
bigdataviewer
Tags: #<Tag:0x00007fd540b0c940> #<Tag:0x00007fd540b0c7d8>

#1

Is there a way in the BigSticher plugin allowing to define the tile positions from the filenames (e.g. ‘Tile_x003_y004.tif’) or do this indirectly (as in the grid/collection stitching plugin option ‘positions from file’?

Thanks to Preibisch et al. for providing this great tool!


#2

Perhaps @tpietzsch or @StephanPreibisch or @hkmoon can assist in this?

eta


#3

Hi, the Autoloader (Define new dataset, choose autoloader) should support this already. You can arrange the tiles later in the BigSticher if necessary. Let me know if you run into problems.

Cheers,
Stephan


#4

Thank you! I will try it out.

Cheers,
Moritz


#5

Dear Stephan,

I tried all options including autoloader. The regular-grid options do not work, as my datasets are not in square shapes. In other words some places in the regular grid are empty. The wildcard parsing options give me only one variable (tile) and not two for x and y position. I did not find an option to specify the tile locations from metadata. I only found the manual shifting of tiles. Am I overlooking something?
On http://imagej.net/BigStitcher_AutoLoader the subsection under the title Patterns in filenames is missing unfortunately.

Thank you in advance and all the best,
Moritz


#6

Dear all,

An update: There is a this function available in BigSticher now! It is documented here: https://imagej.net/BigStitcher_manual_translation

Many thanks to David Hörl (hoerldavid) and Stephan Preibisch (StephanPreibisch)

Best Moritz