no initial angle rotation with newer Fiji/ big stitcher versions

[JanaFuhrmann]

Hi,

I have been using the big stitcher and the multi view reconstruction plugin for processing of multi angle .czi files for a few years now and I noticed lately that with newer Fiji versions it does not take the initial rotation (imaging angles) from the metadata anymore. And now I have to manually rotate each image in big stitcher before aligning them. (I work without beads so I do some manual alignment afterwards anyways, but it takes more time now that I also have to apply the rotations myself.) Is there a workaround for that problem?

I run the following macros for defining and resaving it as h5

run("Define dataset ...", "define_dataset=[Zeiss Lightsheet Z.1 Dataset Loader (Bioformats)] project_filename="+ define_xml +" first_czi="+ input_czi +" channel_1=488 channel_2=561 _______illumination_1=0 apply_rotation_to_dataset fix_bioformats dataset_save_path=" + input_czi);
run("As HDF5 ...", "select="+ input_data +" resave_angle=[All angles] resave_channel=[All channels] resave_illumination=[All illuminations] resave_tile=[All tiles] resave_timepoint=[All Timepoints] subsampling_factors=[{ {1,1,1}, {2,2,1}, {4,4,2}, {8,8,4} }] hdf5_chunk_sizes=[{ {16,16,16}, {16,16,16}, {16,16,16}, {16,16,16} }] timepoints_per_partition=1 setups_per_partition=0 use_deflate_compression export_path="+ input_data +"");

I would very much appreciate your help with that.

Thanks in advance

Jana