Processing split data

I. Processing Video Sessions Split Into Multiple Files

It is common for continuous calcium imaging data to be saved across multiple video files for easier access. For example as follows:

◼ My_data
├─ Session_1_day_0
│  ├─ 0.avi
│  ├─ 1.avi
│  ├─ ...
│  └─ 12.avi
├─ Session_2_day_5
│  ├─ 0.avi
│  ├─ 1.avi
│  ├─ ...
│  └─ 14.avi
└─ Session_3_day_15
   ├─ 0.avi
   ├─ 1.avi
   ├─ ...
   └─ 14.avi

Treating each of these split videos as independent sessions is not ideal, as using the inter-session alignment pipeline is more computationally demanding than simply aligning and motion-correcting the concatenated chunk.

The recommended approach is to select the parent folder when calling:

CaliAli_options = CaliAli_downsample(CaliAli_options);

This will generate three .mat files—one for each session—containing the data from all individual segments concatenated. By default, CaliAli searches for .avi files and concatenates them using natural sorting based on their filenames. The output will look like:

◼ My_data
├─ Session_1_day_0
├─ Session_2_day_5
├─ Session_3_day_15
├─ Session_1_day_0_con.mat
├─ Session_1_day_5_con.mat
└─ Session_3_day_15_con.mat

video_app

What about video sessions split into multiple TIFF files?

You can set the CaliAli parameter CaliAli_options.downsampling.file_extension = 'tiff'.

The simplest way is to modify the demo options:

 edit CaliAli_demo_parameters

and set params.file_extension = 'tiff';. This will tell CaliAli to search for tiff files.