stripe artifacts with "write to disk" about stitching HOT 4 CLOSED

I checked some recent stitching results obtained using this plugin with the Write to disk option via PyImagJ. They do not seem to have this artifact.

Single channel multiphoton:

A brighter example:

RGB image:

The yellow box marks the boundary of a tile.
The same image from the first example stitched with the the Fuse to display option in ImageJ:

Overall the transition between boundaries looks quite smooth.

A snippet of the code I used:

    params = {'type': 'Positions from file', 'order': 'Defined by TileConfiguration', 
            'directory':stitch_folder, 'ayout_file': 'TileConfiguration.txt', 
            'fusion_method': 'Linear Blending', 'regression_threshold': '0.30', 
            'max/avg_displacement_threshold':'2.50', 'absolute_displacement_threshold': '3.50', 
            'compute_overlap':False, 'computation_parameters': 'Save computation time (but use more RAM)', 
            'image_output': 'Write to disk', 'output_directory': temp_channel_folder}
    plugin = "Grid/Collection stitching"
    ij.py.run_plugin(plugin, params)

from stitching.

@schmiedc @ctrueden is this still the case?
People are using image_output=[Write to disk] in various examples, see e.g. https://github.com/uw-loci/automatic-histology-registration-pyimagej/blob/8ad405170ec46dccbdc1c20fbbeb6eaff47b8b76/pseudo_modality.ipynb and imagej/pyimagej#192.

If the outputs of image_output=[Fuse and display] and image_output=[Write to disk] differ, we should warn and recommend using the Fusion.fuse API directly where possible.

from stitching.

@imagejan I'm sorry, I don't know.

@binli123 Heads up: your workflows that use the Grid/Collection stitching's "Write to disk" feature might be writing out suboptimal data, compared to using "Fuse and display" in memory. Would it be easy for you to check this?

from stitching.

Great, thanks @binli123! I will close this then. We can reopen if anyone has a recipe to reproduce with the latest version.

from stitching.