************** CELLFINDER LOG ************** Analysis carried out: 2021-10-25_16-18-39 Output directory: C:/Users/RieraLab/Desktop/Pedja/Output Current directory: C:\Users\RieraLab Version: 0.4.19 ************** GIT INFO ************** Gitpython is not installed. Cannot check if software is in a git repository ************** COMMAND LINE ARGUMENTS ************** Command: C:\Users\RieraLab\anaconda3\envs\cellfinder\Scripts\cellfinder Input arguments: ['-s', 'C:/Users/RieraLab/Desktop/Pedja/brain/c1/Brain9/22-51-21_brain9 new_UltraII_C1_Z0000.tif', '-b', 'C:/Users/RieraLab/Desktop/Pedja/brain/c0/Brain9/22-51-21_brain9 new_UltraII_C0_Z0000.tif', '-o', 'C:/Users/RieraLab/Desktop/Pedja/Output', '-v', '5', '2', '2', '--orientation', 'asl'] ************** VARIABLES ************** Namespace: signal_planes_paths: ['C:/Users/RieraLab/Desktop/Pedja/brain/c1/Brain9/22-51-21_brain9 new_UltraII_C1_Z0000.tif'] background_planes_path: ['C:/Users/RieraLab/Desktop/Pedja/brain/c0/Brain9/22-51-21_brain9 new_UltraII_C0_Z0000.tif'] output_dir: C:/Users/RieraLab/Desktop/Pedja/Output signal_ch_ids: None background_ch_id: None registration_config: C:\Users\RieraLab\anaconda3\envs\cellfinder\lib\site-packages\cellfinder_core\config\cellfinder.conf.custom voxel_sizes: ['5', '2', '2'] network_voxel_sizes: [5, 1, 1] no_detection: False no_classification: False no_register: False no_analyse: False no_figures: False start_plane: 0 end_plane: -1 save_planes: False outlier_keep: False artifact_keep: False max_cluster_size: 100000 soma_diameter: 16 ball_xy_size: 6 ball_z_size: 15 ball_overlap_fraction: 0.6 log_sigma_size: 0.2 n_sds_above_mean_thresh: 10 soma_spread_factor: 1.4 trained_model: None model_weights: None network_depth: 50 batch_size: 32 cube_width: 50 cube_height: 50 cube_depth: 20 save_empty_cubes: False n_free_cpus: 2 max_ram: None save_csv: False debug: False sort_input_file: False no_models: False model: resnet50_tv heatmap_smooth: 100 mask_figures: True install_path: C:\Users\RieraLab\.cellfinder download_path: C:\Users\RieraLab\AppData\Local\Temp\tmpkwa0yii9 no_amend_config: False atlas: allen_mouse_25um orientation: asl backend: niftyreg affine_n_steps: 6 affine_use_n_steps: 5 freeform_n_steps: 6 freeform_use_n_steps: 4 bending_energy_weight: 0.95 grid_spacing: -10 smoothing_sigma_reference: -1.0 smoothing_sigma_floating: -1.0 histogram_n_bins_floating: 128 histogram_n_bins_reference: 128 Paths: output_dir: C:/Users/RieraLab/Desktop/Pedja/Output registration_output_folder: C:/Users/RieraLab/Desktop/Pedja/Output\registration metadata_path: C:/Users/RieraLab/Desktop/Pedja/Output\cellfinder.json registration_metadata_path: C:/Users/RieraLab/Desktop/Pedja/Output\registration\brainreg.json ************** LOGGING ************** 2021-10-25 16:18:39 PM - INFO - MainProcess fancylog.py:295 - Starting logging 2021-10-25 16:18:39 PM - INFO - MainProcess fancylog.py:296 - Multiprocessing-logging module found. Logging from all processes 2021-10-25 16:18:42 PM - INFO - MainProcess main.py:51 - Registering to atlas 2021-10-25 16:18:42 PM - DEBUG - MainProcess prep.py:307 - Making registration directory 2021-10-25 16:18:44 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use 2021-10-25 16:18:44 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 62 2021-10-25 16:18:44 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 62 2021-10-25 16:18:44 PM - INFO - MainProcess main.py:48 - Loading raw image data 2021-10-25 16:18:44 PM - DEBUG - MainProcess load.py:90 - Data type is: tif stack 2021-10-25 16:18:44 PM - DEBUG - MainProcess load.py:149 - Loading: C:/Users/RieraLab/Desktop/Pedja/brain/c0/Brain9/22-51-21_brain9 new_UltraII_C0_Z0000.tif 2021-10-25 16:18:45 PM - DEBUG - MainProcess load.py:157 - Downsampling stack in X/Y