Primodium Analysis

An analysis workflow for quantifying cellular dynamics during lateral line formation of Zebrafish

editing

Description

Input: Time lapse sequence (Tiff stack) with centrin signal.

Output: centrin coordinates / time points in a text file

The lateral line formation during the development of Zebrafish is organized by a collective cell migration. A group of cells form a cigar-like structure called “primordium” and migrates from tail towards heads, and periodically deposits part of the cells as a cluster, consisteing of upto N cells, that later forms sensory organ. To study how these cell cluster are prepared within primordium, cells were labeld with centrin and their time-lapse sequences were captured.

This script measures all centrin coordinates and measures distance to the “midline” of primordium, thus enabling the quantitative analysis of how centrins converges towards the central axis primordium.

Dependency

ImageJ

Installation

https://github.com/miura/ijmacros/blob/master/K_primodiumV2.ijm

Usages

Repository

https://github.com/miura/ijmacros/blob/master/K_primodiumV2.ijm