Syntax
function params=CaliAli_demo_parameters()
Description
CaliAli_demo_parameters: Define demo parameters for CaliAli processing pipeline.
This function initializes and returns a structure containing default parameters
for data preprocessing, motion correction, inter-session alignment, and neuronal
extraction using CNMF-E.
None
Function Outputs:
| Parameter Name |
Type |
Description |
| params |
Structure |
All default parameters for CaliAli processing. |
Example usage:
CaliAli_Options = CaliAli_demo_parameters();
Parameters
📌 Data Preprocessing Parameters
| Parameter Name |
Value |
Description |
gSig |
2.5 |
Gaussian filter size for neurons (pixels) |
sf |
10 |
Frame rate (fps) |
BVsize |
[] |
Size of blood vessels (pixels) [min diameter, max diameter]. Default is calculated based on gSig. |
spatial_ds |
1 |
Spatial downsampling factor |
temporal_ds |
1 |
Temporal downsampling factor |
neuron_enhance |
true |
Enhance neurons using MIN1PIE background subtraction |
noise_scale |
true |
Scale noise for each pixel |
detrend |
1 |
Detrending window (seconds). 0 = no detrending |
file_extension |
'avi' |
If a folder is selected instead of a single video file, concatenate all videos with the specified file extension within that folder. |
📌 Motion Correction Parameters
| Parameter Name |
Value |
Description |
do_non_rigid |
false |
Perform non-rigid motion correction? |
reference_projection_rigid |
'BV' |
Use blood vessels as reference for rigid correction |
non_rigid_pyramid |
{'BV', 'BV', 'neuron'} |
Multi-level registration pyramid |
non_rigid_batch_size |
[20, 60] |
Frame range for parallel processing |
📌 Inter-session Alignment Parameters
| Parameter Name |
Value |
Description |
projections |
'BV+neuron' |
Use both blood vessels and neurons for alignment |
final_neurons |
0 |
Perform an extra neuron alignment iteration? |
Force_BV |
false |
Force blood vessel use even if deemed unusable |
| Parameter Name |
Value |
Description |
frames_per_batch |
0 |
Number of frames per batch. 0 = process each session as a single batch |
memory_size_to_use |
256 |
Memory allowed for MATLAB (GB) |
memory_size_per_patch |
16 |
Memory for each patch (GB) |
patch_dims |
[64, 64] |
Patch dimensions |
with_dendrites |
true |
Include dendrites in the model |
search_method |
'dilate' |
Search method ('dilate' or 'ellipse') |
spatial_constraints |
struct('connected', false, 'circular', false) |
Spatial constraints |
spatial_algorithm |
'hals_thresh' |
Spatial extraction algorithm |
📌 Deconvolution Parameters
| Parameter Name |
Value |
Description |
deconv_options.type |
'ar1' |
Calcium trace model ('ar1' or 'ar2') |
deconv_options.method |
'foopsi' |
Deconvolution method |
deconv_options.smin |
-5 |
Minimum spike size |
deconv_options.optimize_pars |
true |
Optimize AR parameters |
deconv_options.optimize_b |
true |
Optimize baseline |
deconv_options.max_tau |
100 |
Max decay time (frames) |
📌 Background Modeling Parameters
| Parameter Name |
Value |
Description |
background_model |
'ring' |
Background model |
nb |
1 |
Number of background components |
bg_neuron_factor |
1.5 |
Background-neuron interaction factor |
ring_radius |
[] |
Will be calculated later |
num_neighbors |
[] |
Number of neighbors for each neuron |
bg_ssub |
2 |
Background downsampling factor |
📌 Merging & Seeding Parameters
| Parameter Name |
Value |
Description |
merge_thr |
0.65 |
Merging threshold |
method_dist |
'max' |
Distance calculation method |
dmin |
5 |
Minimum distance between neurons |
merge_thr_spatial |
[0.8, 0.4, -inf] |
Spatial merging threshold |
min_corr |
0.2 |
Minimum correlation for seeding |
min_pnr |
4 |
Minimum peak-to-noise ratio for seeding |