timelapse_nuclei_to_track: 'timelapse_second_dataset'
timelapse_membrane_to_track: 'timelapse_second_dataset'
base_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/'


dual_channel_split_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/split_nuclei_membrane_raw/'
timelapse_nuclei_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/nuclei_timelapses/'
timelapse_seg_nuclei_directory : '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/seg_nuclei_timelapses/'
timelapse_seg_nuclei_vollseg_directory : '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/seg_nuclei_vollseg_timelapses/'
timelapse_membrane_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/membrane_timelapses/'
timelapse_seg_membrane_directory : '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/seg_membrane_timelapses_fixed/'
timelapse_oneat_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/oneat_detections/'
timelapse_oneat_vollseg_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/oneat_vollseg_detections/'
timelapse_region_of_interest_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/region_of_interest/'
tracking_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/nuclei_membrane_tracking/'
tracking_vollseg_directory: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/nuclei_vollseg_membrane_tracking/'
variable_t_calibration: {160: 182, 260: 283}
voxel_size_xyz: [0.6918, 0.6918, 2]
oneat_nuclei_csv_file: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/oneat_detections/non_maximal_oneat_mitosis_locations_nuclei_timelapse_second_dataset.csv'
oneat_membrane_csv_file: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/oneat_detections/non_maximal_oneat_mitosis_locations_membrane_timelapse_second_dataset.csv'
oneat_nuclei_vollseg_csv_file: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/oneat_vollseg_detections/non_maximal_oneat_mitosis_locations_nuclei_vollseg_timelapse_second_dataset.csv'

goblet_cells_nuclei_predicted: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_predicted/goblet_cells_nuclei_annotations_inception.csv'
basal_cells_nuclei_predicted: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_predicted/basal_cells_nuclei_annotations_inception.csv'
radial_cells_nuclei_predicted: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_predicted/radially_intercalating_cells_nuclei_annotations_inception.csv'

goblet_cells_nuclei_gt: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations/goblet_cells_nuclei_annotations.csv'
basal_cells_nuclei_gt: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations/basal_cells_nuclei_annotations.csv'
radial_cells_nuclei_gt: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations/radially_intercalating_cells_nuclei_annotations.csv'

goblet_cells_membrane_predicted: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_predicted/goblet_cells_membrane_annotations_inception.csv'
basal_cells_membrane_predicted: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_predicted/basal_cells_membrane_annotations_inception.csv'
radial_cells_membrane_predicted: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_predicted/radially_intercalating_cells_membrane_annotations_inception.csv'

goblet_cells_membrane_transferred: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_transferred/goblet_cells_membrane_annotations_inception.csv'
basal_cells_membrane_transferred: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_transferred/basal_cells_membrane_annotations_inception.csv'
radial_cells_membrane_transferred: '/lustre/fsn1/projects/rech/jsy/uzj81mi/Mari_Data_Oneat/Mari_Second_Dataset_Analysis/annotations_transferred/radially_intercalating_cells_membrane_annotations_inception.csv'