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feat(imaging): write bigtiff for caiman processing for bruker files #178

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merged 5 commits into from
Jan 29, 2024
Merged

feat(imaging): write bigtiff for caiman processing for bruker files #178

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1a8bc68
Update setup.py
Sep 6, 2023
a5b2e89
feat(imaging): write bigtiff for caiman processing for bruker files
Jan 29, 2024
087c10b
Merge remote-tracking branch 'upstream/caiman_per_plane_processing' i…
Jan 29, 2024
50b3754
style(imaging)
Jan 29, 2024
bce6edf
update(setup): revert bad merge conflict
Jan 29, 2024
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35 changes: 21 additions & 14 deletions element_calcium_imaging/imaging_no_curation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -464,28 +464,35 @@ def make(self, key):
channel = caiman_params.get("channel_to_process", 0)

if ndepths == 1: # single-plane processing
if nchannels > 1:
if acq_software == "ScanImage":
if acq_software == "ScanImage":
if nchannels > 1:
# handle multi-channel tiff image before running CaImAn
tmp_dir = pathlib.Path(output_dir) / "channel_separated_tif"
tmp_dir.mkdir(exist_ok=True)
_process_scanimage_tiff(
[f.as_posix() for f in image_files], output_dir=tmp_dir
)
image_files = tmp_dir.glob(f"*_chn{channel}.tif")
elif acq_software == "PrairieView":
from element_interface.prairie_view_loader import (
PrairieViewMeta,
)
elif acq_software == "PrairieView":
from element_interface.prairie_view_loader import (
PrairieViewMeta,
)

pv_dir = pathlib.Path(image_files[0]).parent
PVmeta = PrairieViewMeta(pv_dir)
image_files = [
pv_dir / f
for f in PVmeta.get_prairieview_files(
channel=caiman_params.get("channel_to_process", 0),
)
]
pv_dir = pathlib.Path(image_files[0]).parent
PVmeta = PrairieViewMeta(pv_dir)
channel = (
channel
if PVmeta.meta["num_channels"] > 1
else PVmeta.meta["channels"][0]
)
image_files = [
PVmeta.write_single_bigtiff(
plane_idx=0,
channel=channel,
output_dir=output_dir,
caiman_compatible=True,
)
]

run_caiman(
file_paths=[f.as_posix() for f in image_files],
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