samilcase
commented
1 year ago I'm new to suite2P as well and having this exact same issue...
{'data_path': ['C:/Users/slca230/Downloads'], 'subfolders': [], 'save_path0': 'C:/Users/slca230/Downloads', 'fast_disk': 'C:/Users/slca230/Downloads', 'input_format': 'tif'} tif Found 1 tifs - converting to binary 2000 frames of binary, time 3.47 sec. 4000 frames of binary, time 6.32 sec. time 7.18 sec. Wrote 4500 frames per binary for 1 planes
PLANE 0 <<<<<<<<<<<<<<<<<<<<<< NOTE: not registered / registration forced with ops['do_registration']>1 (no previous offsets to delete) NOTE: applying default C:\Users\slca230.suite2p\classifiers\classifier_user.npy ----------- REGISTRATION Reference frame, 11.13 sec. Registered 500/4500 in 10.53s Registered 1000/4500 in 20.50s Registered 1500/4500 in 30.33s Registered 2000/4500 in 40.18s Registered 2500/4500 in 50.05s Registered 3000/4500 in 59.83s Registered 3500/4500 in 69.72s Registered 4000/4500 in 79.23s Registered 4500/4500 in 89.19s ----------- Total 105.07 sec Registration metrics, 16.53 sec. ----------- ROI DETECTION Binning movie in chunks of length 10 Binned movie of size [450,319,552] created in 3.90 sec. ERROR<<< Traceback (most recent call last): File "C:\Users\slca230\Anaconda3\lib\runpy.py", line 197, in _run_module_as_main ERROR<<< return _run_code(code, main_globals, None, File "C:\Users\slca230\Anaconda3\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\slca230\suite2p\suite2p__main.py", line 78, in
main() File "C:\Users\slca230\suite2p\suite2p\ main__.py", line 71, in main run_s2p(ops, db) File "C:\Users\slca230\suite2p\suite2p\run_s2p.py", line 443, in run_s2p op = run_plane(op, ops_path=ops_path) File "C:\Users\slca230\suite2p\suite2p\run_s2p.py", line 296, in run_plane ERROR<<< ops = pipeline(f_reg, f_raw, f_reg_chan2, f_raw_chan2, run_registration, ops, stat=stat) File "C:\Users\slca230\suite2p\suite2p\run_s2p.py", line 129, in pipeline ops, stat = detection.detection_wrapper(f_reg, File "C:\Users\slca230\suite2p\suite2p\detection\detect.py", line 148, in detection_wrapper stat = select_rois( File "C:\Users\slca230\suite2p\suite2p\detection\detect.py", line 202, in select_rois ERROR<<< new_ops, stat = sparsedetect.sparsery( File "C:\Users\slca230\suite2p\suite2p\detection\sparsedetect.py", line 307, in sparsery scale, estimate_mode = find_best_scale(I=I, spatial_scale=spatial_scale) File "C:\Users\slca230\suite2p\suite2p\detection\sparsedetect.py", line 266, in find_best_scale scale = estimate_spatial_scale(I=I) File "C:\Users\slca230\suite2p\suite2p\detection\sparsedetect.py", line 256, in estimate_spatialscale im, = mode(imap[ipk][isort[:50]], keepdims=True) TypeError: mode() got an unexpected keyword argument 'keepdims' Interrupted by error (not finished)
chriski777
cgaletzka
JAMoreno-Larios
Hi,
I am a new suite2p user with very little python familiarity. I am currently collecting a data set capturing live GCaMP6f activity in human brain organoids (imaged on a confocal microscope, not a 2-photon) and am very interested in assessing the suitability of the suite2p analysis pipeline for my data.
To start, I have attempted to run a provided example data set to get things up and running however I am coming across the below error message (also attached).
I would appreciate any suggested fixes.
Many thanks,
{'data_path': ["C:/Users/60288184/OneDrive - Children's Medical Research Institute/KR/SNAP25 Project/Calcium Imaging/Suite2Pfiles/Data_path"], 'subfolders': [], 'save_path0': "C:/Users/60288184/OneDrive - Children's Medical Research Institute/KR/SNAP25 Project/Calcium Imaging/Suite2Pfiles/Save_path", 'fast_disk': "C:/Users/60288184/OneDrive - Children's Medical Research Institute/KR/SNAP25 Project/Calcium Imaging/Suite2Pfiles/Fast_path", 'input_format': 'tif'} tif Found 1 tifs - converting to binary 2000 frames of binary, time 19.39 sec. time 19.49 sec. Wrote 2000 frames per binary for 1 planes PLANE 0 <<<<<<<<<<<<<<<<<<<<<< NOTE: not registered / registration forced with ops['do_registration']>1 (no previous offsets to delete) NOTE: applying default C:\Users\60288184.suite2p\classifiers\classifier_user.npy ----------- REGISTRATION Reference frame, 42.34 sec. Registered 500/2000 in 460.11s Registered 1000/2000 in 1019.69s Registered 1500/2000 in 1465.94s Registered 2000/2000 in 1951.87s ----------- Total 2007.89 sec Registration metrics, 356.56 sec. ----------- ROI DETECTION Binning movie in chunks of length 10 Binned movie of size [200,656,776] created in 6.83 sec.
220929_example data_error_downgradedpython to 3.8.txt