I use the same dataset but have a problem of "Array must not contain infs or NaNs" in 1.1.0
ops = default_ops()
ops.update(
{
"nplanes": 1,
"nchannels": 1,
"functional_chan": 1,
"fs": float(settings["frame_rate"] or 10.0),
"tau": 1,
# "do_bidiphase": True,
"do_registration": True,
"nonrigid": True,
"roidetect": True,
"spikedetect": True,
"delete_bin": False,
"save_mat": True,
"batch_size": 500,
"max_iterations": 100,
# "threshold_scaling": 0.5,
# "spatial_scale": 1,
"extract_patches": True,
# "smooth_sigma_time": 1.0,
# "two_step_registration": True
# "diameter": [10]
}
)
D:\free moving 2p\PhD\free moving 2p\data_analysis\run_suite2p_cellvideo_260518.py'
Running Suite2p
Input: D:\free moving 2p\PhD\free moving 2p\data_analysis\data\260518-2-2_2026-05-19_19-06-27\CellVideo1\CellVideo
Output: D:\free moving 2p\PhD\free moving 2p\data_analysis\data\260518-2-2_2026-05-19_19-06-27\CellVideo1\suite2p_CellVideo1
Frame rate: 9.21 Hz
C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py:184: RuntimeWarning: invalid value encountered in divide
dy, dx = np.meshgrid(np.arange(-d0[0]*3, d0[0]*3 + 1) / d0[0],
C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py:185: RuntimeWarning: invalid value encountered in divide
np.arange(-d0[1]*3, d0[1]*3 + 1) / d0[1], indexing="ij")
C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py:205: RuntimeWarning: divide by zero encountered in divide
dists = (((ypix - med[0]) / d0[0])**2 + ((xpix - med[1]) / d0[1])**2)**0.5
C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py:205: RuntimeWarning: invalid value encountered in divide
dists = (((ypix - med[0]) / d0[0])**2 + ((xpix - med[1]) / d0[1])**2)**0.5
C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py:67: RuntimeWarning: divide by zero encountered in divide
y = y / dy
C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py:68: RuntimeWarning: divide by zero encountered in divide
x = x / dx
C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py:79: RuntimeWarning: invalid value encountered in subtract
yx = (yx - mu[:, np.newaxis]) * lam**.5
Backend qtagg is interactive backend. Turning interactive mode on.
Traceback (most recent call last):
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\runpy.py", line 86, in _run_code
exec(code, run_globals)
File "c:\Users\TsingSV\.vscode\extensions\ms-python.debugpy-2026.6.0-win32-x64\bundled\libs\debugpy\__main__.py", line 71, in <module>
cli.main()
File "c:\Users\TsingSV\.vscode\extensions\ms-python.debugpy-2026.6.0-win32-x64\bundled\libs\debugpy/..\debugpy\server\cli.py", line 542, in main
run()
File "c:\Users\TsingSV\.vscode\extensions\ms-python.debugpy-2026.6.0-win32-x64\bundled\libs\debugpy/..\debugpy\server\cli.py", line 361, in run_file
runpy.run_path(target, run_name="__main__")
File "c:\Users\TsingSV\.vscode\extensions\ms-python.debugpy-2026.6.0-win32-x64\bundled\libs\debugpy\_vendored\pydevd\_pydevd_bundle\pydevd_runpy.py", line 310, in run_path
return _run_module_code(code, init_globals, run_name, pkg_name=pkg_name, script_name=fname)
File "c:\Users\TsingSV\.vscode\extensions\ms-python.debugpy-2026.6.0-win32-x64\bundled\libs\debugpy\_vendored\pydevd\_pydevd_bundle\pydevd_runpy.py", line 127, in _run_module_code
_run_code(code, mod_globals, init_globals, mod_name, mod_spec, pkg_name, script_name)
File "c:\Users\TsingSV\.vscode\extensions\ms-python.debugpy-2026.6.0-win32-x64\bundled\libs\debugpy\_vendored\pydevd\_pydevd_bundle\pydevd_runpy.py", line 118, in _run_code
exec(code, run_globals)
File "D:\free moving 2p\PhD\free moving 2p\data_analysis\run_suite2p_cellvideo_260518.py", line 28, in <module>
main()
File "D:\free moving 2p\PhD\free moving 2p\data_analysis\run_suite2p_cellvideo_260518.py", line 15, in main
run_suite2p_session(
File "D:\free moving 2p\PhD\free moving 2p\data_analysis\src\twop_analysis\suite2p_runner.py", line 114, in run_suite2p_session
return run_s2p(db,ops )
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\run_s2p.py", line 459, in run_s2p
outputs = run_plane(db=db, settings=settings, db_path=db_path)
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\run_s2p.py", line 303, in run_plane
outputs = pipeline(db["save_path"], f_reg, f_raw, f_reg_chan2, f_raw_chan2,
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\pipeline_s2p.py", line 156, in pipeline
detect_outputs, stat, redcell = detection.detection_wrapper(f_reg,
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\detect.py", line 255, in detection_wrapper
stat = roi_stats(stat, Ly, Lx, diameter=diameter,
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py", line 211, in roi_stats
radii = fitMVGaus(ypix, xpix, lam, dy=d0[0], dx=d0[1], thres=2)[2]
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\suite2p\detection\stats.py", line 83, in fitMVGaus
radii, evec = np.linalg.eig(cov)
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\numpy\linalg\_linalg.py", line 1465, in eig
_assert_finite(a)
File "C:\Users\TsingSV\.conda\envs\data_analysis\lib\site-packages\numpy\linalg\_linalg.py", line 207, in _assert_finite
raise LinAlgError("Array must not contain infs or NaNs")
numpy.linalg.LinAlgError: Array must not contain infs or NaNs
The newest verision 1.1.0.
Describe the issue:
I use the same dataset but have a problem of "Array must not contain infs or NaNs" in 1.1.0
Reproduce the code example:
Example input dataset used to reproduce the issue:
detect gcamp7f soma
Error message:
Version information:
The newest verision 1.1.0.
Context for the issue:
No response