Movie Definition (movie_definition)¶

image_type (string) — Movie format.

Option Movie Format

‘seq’ Image Sequences (Individual Images)

‘stack’ Image Stacks (Multi-Page Images)

‘nd2’ Nikon ND2 Format
image_path (nx1 cell array) — Path to the folder storing the images.
Image Sequences/Stacks
Each row stores the path to the folder for the i-th channel.
Example

Example 1. A movie has three channels: CFP, YFP, and mCherry. Images of these channels locate in X:/tracking_code/raw_images/CFP/, X:/tracking_code/raw_images/YFP/, and X:/tracking_code/raw_images/mCherry/, respectively.
image_path = {'X:/tracking_code/raw_images/CFP/'; 'X:/tracking_code/raw_images/YFP/'; 'X:/tracking_code/raw_images/mCherry/'};
List the paths of different channels separately, even if all the images locate in the same folder.

Example 2. A movie has 3 channels: CFP, YFP, and mCherry. All the images locate in X:/tracking_code/raw_images/.
image_path = {'X:/tracking_code/raw_images/'; 'X:/tracking_code/raw_images/'; 'X:/tracking_code/raw_images/'};
image_path should always be a cell array.

Example 3. A movie only has the CFP channel. Images locate in X:/tracking_code/raw_images/.
image_path = {'X:/tracking_code/raw_images/'};
Nikon ND2 Format
Each row stores the path to the folder for the i-th segment.
Example

A movie is stored in two segments, locating in X:/tracking_code/raw_images/seg1/ and X:/tracking_code/raw_images/seg2/, respectively.
image_path = {'X:/tracking_code/raw_images/seg1/'; 'X:/tracking_code/raw_images/seg2/'};

Formatting the Paths

For cross-platform compatibility, EllipTrack requires all paths to use forward slashes (/) rather than backward slashes (\). Paths to folders should end with a forward slash.

Example 1. Path to a folder.

Incorrect format. Use backward slashes rather than forward slashes; no forward slash at the end of the path.

path = 'X:\tracking_code\raw_images';

Correct format.

path = 'X:/tracking_code/raw_images/';

Example 2. Path to a MAT file.

Incorrect format. Use backward slashes rather than forward slashes; use forward slash at the end of the path.

path = 'X:\tracking_code\mat_files\cmosoffset.mat/';

Correct format.

path = 'X:/tracking_code/mat_files/cmosoffset.mat';

EllipTrack automatically adjusts all paths to the correct format, though manual formatting is strongly suggested.

filename_format (string) – Formats of image filenames.

Filenames are specified with MATLAB FormatSpec. Available conversion specifiers include

Specifier	Data Type	Availability
%r	Row ID, Number	All movie formats
%a	Row ID, Letter (lower case)	All movie formats
%b	Row ID, Letter (upper case)	All movie formats
%c	Column ID, Number	All movie formats
%s	Site ID, Number	Image sequences/stacks
%i	Channel ID, Number.	Image sequences/stacks
%n	Channel Name, String.	Image sequences/stacks
%t	Frame ID. Number.	Image sequences

Field widths can be specified. For example, %03t indicates that Frame ID has a minimal length of three digits, filled with prefix 0. This specifier will be converted to 001, 100, and 1000 for Frame 1, 100, and 1000.

Full filenames should be specified for image sequences/stacks. A prefix is sufficient for the Nikon ND2 format.

Example

Example 1 (Image Sequences). Filenames follow the convention RowID_ColumnID_SiteID_ChannelName_FrameID.tif. Frame ID has a minimal length of three digits, filled with prefix 0. For example, 1_2_3_CFP_004.tif.

filename_format = '%r_%c_%s_%n_%03t.tif';

Example 2 (Nikon ND2 Format). Filenames follow the convention WellRowIDColumnID_CFP,YFP,mCherry_Seq00XX.nd2. Row ID is an upper-case letter; Column ID is a two-digit number, filled with prefix 0; and XX represents an arbitrary number. For example, WellA02_CFP,YFP,mCherry_Seq0001.nd2.

filename_format = 'Well%b%02c';

Note that this parameter only defines the format of image filenames, not the actual values of Row ID, Frame ID, etc. These values will be defined by the parameters below.

channel_names (nx1 cell array) — Name of the fluorescence channels

Each row stores the name of the i-th channel. For image sequences/stacks, they must match the order of image_path. The first channel must image cell nuclei.
signal_names (nx1 cell array) — Names of the signals to measure

Each row stores the name of the i-th signal. Must match the order of channel_names.
if_compute_cytoring (nx1 binary array) — Whether to compute signals in the cytoplasmic ring.

Each row is an indicator variable (1 for compute, 0 for not compute) for the i-th channel. Must match the order of channel_names. The first element must be 0.
bias_paths (nx1 cell array) — Paths to the MAT files storing the illumination biases.

Each row stores the path for the i-th channel. Must match the order of channel_names.

Example

A movie has three channels: CFP, YFP, and mCherry, with the following information.

Channel	Signal	Cyto Ring?	Path to Bias
CFP	H2B	No	`X:/tracking_code/bias/CFP.mat`
YFP	CDK2 Sensor	Yes	`X:/tracking_code/bias/YFP.mat`
mCherry	ERK Sensor	Yes	`X:/tracking_code/bias/mCherry.mat`

channel_names = {'CFP';
                 'YFP';
                 'mCherry'};

signal_names = {'H2B';
                'CDK2';
                'ERK'};

if_compute_cytoring = [0;
                       1;
                       1];

bias_paths = {'X:/tracking_code/bias/CFP.mat';
              'X:/tracking_code/bias/YFP.mat';
              'X:/tracking_code/bias/mCherry.mat'};

cmosoffset_path (string) — Path to the MAT file storing the camera dark noises.
wells_to_track (nx3 integer array) — Movie coordinates in a multi-well plate.

Each row stores the Row, Column, and Site ID of one movie. Use [1, 1, 1] if the experiment is not performed in a multi-well plate.
frames_to_track (integer array) — Frame IDs to track.

Frame IDs do not need to be consecutive. Can start from zero.

jitter_correction_method (string) — Method of Jitter Correction.

Option

Description

Suggested Situation

‘none’

No Jitter Correction is performed.

Jitters are negligible.

‘local’

Jitters are calculated from each movie

independently.

Movies are not captured

on the same multi-well plate.

‘global’

Jitters are calculated from the plate

motion jointly inferred from all movies.

Movies are captured on

the same multi-well plate.

Require at least 6 movies.

num_cores (integer) — Number of local cores for parallel computing.

Option	Movie Format
‘seq’	Image Sequences (Individual Images)
‘stack’	Image Stacks (Multi-Page Images)
‘nd2’	Nikon ND2 Format