This release introduces a tool that utilizes cellpose-generated masks from the astroglial-segmentation package to perform detailed subsegmentation and alignment of cellular regions. Each subsegment is assigned a unique segment number based on its calculated distance from the ventricular lining, allowing for a highly organized spatial structure of cellular subregions.
Output Data Structure
The output consists of two matrices that capture essential details for each subsegment:
1. Trace Matrix
This matrix captures the intensity trace data over multiple time points (or frames) for each subsegment. Each row represents a subsegment associated suite2p ROI index s2p, with a segment label S, and contains intensity values f1, f2, ... fF, where each f corresponds to a specific time point or frame.
s2p
S1
f1
f2
...
fF
s2p
S2
f1
f2
...
fF
...
S: Segment label
f1, f2, ... fF: Intensity traces across frames
2. Coordinate Matrix
This matrix provides detailed spatial data for each subsegment, including both original and aligned pixel coordinates for precise positioning. It includes identifiers such as the suite2p ROI index s2p, cell label C, segment label S, and subsegment number S_#x. The coordinate pairs (xo, yo) and (xa, ya) represent the original and aligned positions, respectively, with a class label indicating the subsegment's classification.
s2p
C1
S1
S_#x
xo1
yo1
xa1
ya1
class
s2p
C1
S1
S_#x
xo2
yo2
xa2
ya2
class
...
s2p: Suite2p ROI index
C: Cell label from cellpose
S: Segment label from cellpose
S_#x: Subsegment number
(xo, yo): Original pixel coordinates
(xa, ya): Aligned pixel coordinates
class: Subsegment classification label
1: complete cell upper part
2: complete cell lower part
3: orphan process upper part
4: orphan process lower part
These structured outputs enable in-depth analysis of subregional distribution and neural activity patterns within segmented regions, aiding in advanced cellular and anatomical studies and are saved as .matfiles
Tool Description
This release introduces a tool that utilizes cellpose-generated masks from the
astroglial-segmentationpackage to perform detailed subsegmentation and alignment of cellular regions. Each subsegment is assigned a unique segment number based on its calculated distance from the ventricular lining, allowing for a highly organized spatial structure of cellular subregions.Output Data Structure
The output consists of two matrices that capture essential details for each subsegment:
1. Trace Matrix
This matrix captures the intensity trace data over multiple time points (or frames) for each subsegment. Each row represents a subsegment associated suite2p ROI index
s2p, with a segment labelS, and contains intensity valuesf1, f2, ... fF, where eachfcorresponds to a specific time point or frame.2. Coordinate Matrix
This matrix provides detailed spatial data for each subsegment, including both original and aligned pixel coordinates for precise positioning. It includes identifiers such as the suite2p ROI index
s2p, cell labelC, segment labelS, and subsegment numberS_#x. The coordinate pairs(xo, yo)and(xa, ya)represent the original and aligned positions, respectively, with a class label indicating the subsegment's classification.These structured outputs enable in-depth analysis of subregional distribution and neural activity patterns within segmented regions, aiding in advanced cellular and anatomical studies and are saved as
.matfiles