diff --git a/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml b/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml index e16c76dff..e498b8467 100644 --- a/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml +++ b/studio/app/optinist/wrappers/optinist/visualize_utils/params/roi_fluo_from_hdf5.yaml @@ -1 +1,4 @@ -"" +# This is a temporary measure. Generally, Transpose should be set to True. +# However, when Transpose is set to True, the data coordinates may sometimes be reversed. +# Therefore, it may be switched to False on the screen. +transpose: True diff --git a/studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py b/studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py index 3d9de2291..036df2fa6 100644 --- a/studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py +++ b/studio/app/optinist/wrappers/optinist/visualize_utils/roi_fluo_from_hdf5.py @@ -36,7 +36,11 @@ def roi_fluo_from_hdf5( all_roi = RoiData( np.nanmax(cell_img.data, axis=0), output_dir=output_dir, file_name="all_roi" ) - fluorescence = FluoData(np.transpose(fluo.data), file_name="fluorescence") + + if params["transpose"]: + fluorescence = FluoData(np.transpose(fluo.data), file_name="fluorescence") + else: + fluorescence = FluoData(fluo.data, file_name="fluorescence") if iscell is None: return {"all_roi": all_roi, "fluorescence": fluorescence}