CaliAli Parameters Overview

This table lists all CaliAli parameters, their default values, a brief description, and guidance on how to choose them.

📌 Parameter Table

Parameter Name	Default Value	Description	How to Choose
`gSig`	`2.5`	Neuron filter size in pixels	Use 1/5 of the neuron diameter in pixels. If unsure, opt for smaller values.
`sf`	`10`	Frame rate (fps)	Set to match the acquisition frame rate.
`input_files`	`[]`	Paths to input video files	Leave empty to manually select files.
`output_files`	`[]`	Paths to output video files	Leave empty for default naming (recommended).

Parameter Name	Default Value	Description	How to Choose
`BVsize`	`[]`	Size of blood vessels in pixels [min, max]	Leave empty to automatically calculate based on gSig or use `BV_app` for optimal selection.
`spatial_ds`	`1`	Spatial downsampling factor	Increase for faster processing, decrease for higher resolution.
`temporal_ds`	`1`	Temporal downsampling factor	Increase only if memory constraints prevent full processing.
`file_extension`	`'avi'`	File extension for processed videos organized in folders	Used when sessions are split into multiple files.

Parameter Name	Default Value	Description	How to Choose
`neuron_enhance`	`true`	Use MIN1PIE background subtraction	Keep enabled unless signal loss is observed during preprocessing.
`noise_scale`	`true`	Enable noise scaling per pixel	Keep enabled unless signal loss is observed during preprocessing.
`detrend`	`1`	Detrending window (seconds), 0 = no detrending	Set to the duration of calcium transients in seconds.

Parameter Name	Default Value	Description	How to Choose
`reference_projection_rigid`	`'BV'`	Reference projection for rigid correction	Choose `neuron` if blood vessels are not suitable.
`do_non_rigid`	`false`	Perform non-rigid motion correction	Enable only after confirming rigid correction was insufficient.
`non_rigid_pyramid`	`{'BV','BV','neuron'}`	Multi-level registration pyramid for non-rigid correction	Use default unless BV is unavailable.
`non_rigid_batch_size`	`[20,60]`	Batch size range for non-rigid correction, CaliAli will optimize within this range.	Set as `[2 x sf, 6 x sf]`.

Parameter Name	Default Value	Description	How to Choose
`do_alignment`	`true`	Perform inter-session alignment	Always true unless sessions were pre-aligned. If false, videos will be concatenated without registration.
`projections`	`'BV+neuron'`	Projection method used for alignment	By default, use both blood vessels and neurons for registration. If one is unsuitable, choose either BV or neurons.
`final_neurons`	`false`	Use an additional alignment iteration based on neurons	Enable if session registration was inaccurate. Often not necessary
`Force_BV`	`0`	Force BV alignment even if stability score is low	Sometimes BV stability score may be low as results of a debris in the FOV. Setting this parameter to true would ensure that BV are used for registration

Parameter Name	Default Value	Description	How to Choose
`memory_size_to_use`	`total_system_memory_GB`	Total available memory for computation	Adjust based on available RAM.
`memory_size_per_patch`	`16`	Memory allocated per patch	Adjust based on available RAM and number of patches.
`patch_dims`	`[64, 64]`	Dimensions of patches	Larger patches improve accuracy but increase computation time..
`w_overlap`	`32`	Patch overlap width	Increase if you detect edge artifacts.
`batch_sz`	`0`	Batch size for alignment, 0 = full session	By default, the batch size is set to match the duration of each session. This parameter allows you to define batches in terms of the number of frames instead.

Parameter Name	Default Value	Description	How to Choose
`min_corr`	`0.1`	Minimum correlation for neuron seeding	In most cases, this value is overridden using `CaliAli_set_initialization_parameters(CaliAli_options)`, allowing selection via a GUI. If not using the GUI, increase it to reduce non-neuronal detections or decrease it to detect more neurons.
`min_pnr`	`6`	Minimum peak-to-noise ratio for seeding	Same as `min_corr`.
`min_pixel`	`[]`	Minimum pixel area for neurons	Automatically calculated based on gSig.

Parameter Name	Default Value	Description	How to Choose
`with_dendrites`	`true`	Do not assume that signals are circular during extraction	Always enable for better CNMF convergence and proper dendrite detection.
`spatial_constraints`	`{'connected': False, 'circular': False}`	Constraints for spatial filtering	[Always disable for better CNMF convergence and dendrite identification.]
`spatial_algorithm`	`'hals_thresh'`	Algorithm for spatial extraction	Use default unless alternative extraction methods are needed.

Parameter Name	Default Value	Description	How to Choose
`deconv_flag`	`true`	Enable deconvolution	Use default if unsure. Enable for better temporal resolution.
`deconv_options`	`{'type': 'ar1', 'method': 'foopsi', 'smin': -5, 'optimize_pars': True, 'max_tau': 100}`	Deconvolution settings	Use default parameters to minimize false-positives and computational stability

Parameter Name	Default Value	Description	How to Choose
`merge_thr_spatial`	`[0.8, 0.4, -inf]`	Merge components with highly correlated spatial shapes (`corr=0.8`), moderate temporal correlations of calcium activities (`corr=0.4`), and disregard spikes correlations (`corr=-inf`).	Increase spatial correlation threshold for stricter merging.