BUG: Unable to extract dendritic ROIs

[seethakris]

Describe the issue:

I first ran suite2p with the default ops for extracting dendrites, which resulted in the extracted suite2p ROIs looking like cellular structures

I then re ran with some changes to the parameters, and with denoising. This resulted in sparse noisy ROIs being extracted (attached ops and image). I tried a few other parameters which gave everything in between these two examples but never had any of the dendrites picked up.

The image does have low SNR which could be the reason for the low pick up of ROIs, but I am still able to view dendritic transients above noise level when I run the video on ImageJ. I am just surprised that none of the ROIs I am extracting overlap around the dendritic components in the image. Is there a specific parameter that I am missing to use, if so can it be included in the ops for axon/dendrite capture.

A sample tiff (1000 frames) can be downloaded here: https://uchicago.box.com/s/13ap0t144uvapq3lneef3apqdcbf6wdm

The whole dataset in h5 format (30000 frames) can be downloaded from here: https://uchicago.box.com/s/pulxnw1h2yekft2sdbbfme6vj2twmag8

Thanks for the support!

Reproduce the code example:

Ops.npy

{'suite2p_version': '0.14.3',
 'look_one_level_down': 0.0,
 'fast_disk': '/Users/seethakrishnan/Library/CloudStorage/Box-Box/DendriticData/Goodsubset/AC13/07032023/apical',
 'delete_bin': True,
 'mesoscan': False,
 'bruker': False,
 'bruker_bidirectional': False,
 'h5py': [],
 'h5py_key': 'data',
 'nwb_file': '',
 'nwb_driver': '',
 'nwb_series': '',
 'save_path0': '/Users/seethakrishnan/Library/CloudStorage/Box-Box/DendriticData/Goodsubset/AC13/07032023/apical',
 'save_folder': 'suite2p',
 'subfolders': [],
 'move_bin': False,
 'nplanes': 1,
 'nchannels': 1,
 'functional_chan': 1,
 'tau': 0.7,
 'fs': 30.0,
 'force_sktiff': False,
 'frames_include': -1,
 'multiplane_parallel': 0.0,
 'ignore_flyback': [],
 'preclassify': 0.0,
 'save_mat': False,
 'save_NWB': 0.0,
 'combined': 1.0,
 'aspect': 1.0,
 'do_bidiphase': False,
 'bidiphase': 0.0,
 'bidi_corrected': False,
 'do_registration': 1,
 'two_step_registration': 0.0,
 'keep_movie_raw': False,
 'nimg_init': 300,
 'batch_size': 500,
 'maxregshift': 0.1,
 'align_by_chan': 1,
 'reg_tif': True,
 'reg_tif_chan2': False,
 'subpixel': 10,
 'smooth_sigma_time': 0.0,
 'smooth_sigma': 1.15,
 'th_badframes': 1.0,
 'norm_frames': True,
 'force_refImg': False,
 'pad_fft': False,
 'nonrigid': True,
 'block_size': [128, 128],
 'snr_thresh': 1.2,
 'maxregshiftNR': 5.0,
 '1Preg': False,
 'spatial_hp_reg': 42.0,
 'pre_smooth': 0.0,
 'spatial_taper': 40.0,
 'roidetect': True,
 'spikedetect': True,
 'sparse_mode': True,
 'spatial_scale': 0,
 'connected': True,
 'nbinned': 5000,
 'max_iterations': 20,
 'threshold_scaling': 1.0,
 'max_overlap': 0.75,
 'high_pass': 100.0,
 'spatial_hp_detect': 25.0,
 'denoise': 1.0,
 'anatomical_only': 0,
 'diameter': 0,
 'cellprob_threshold': 0.0,
 'flow_threshold': 1.5,
 'spatial_hp_cp': 0.0,
 'pretrained_model': 'cyto',
 'soma_crop': 1.0,
 'neuropil_extract': True,
 'inner_neuropil_radius': 2,
 'min_neuropil_pixels': 350,
 'lam_percentile': 50.0,
 'allow_overlap': False,
 'use_builtin_classifier': False,
 'classifier_path': '',
 'chan2_thres': 0.65,
 'baseline': 'maximin',
 'win_baseline': 60.0,
 'sig_baseline': 10.0,
 'prctile_baseline': 8.0,
 'neucoeff': 0.7,
 'input_format': 'h5',
}

Error message:

No response

Version information:

0.14.3

Context for the issue:

No response