Pipeline for the 3D shape and cell proliferation analysis in a regenerating axolotl humerus
Authors/Creators
- 1. Universitat Politècnica de Catalunya
- 2. Northeastern University
Contributors
Research group (4):
- 1. Northeastern Unievrsity
- 2. Northeastern University
- 3. Universitat Politècnica de Catalunya
Description
This document describes in detail the process followed in Fiji [1], MATLAB [2] and StarDist-3D [3] to obtain the experimental results shown in the main study available at:
Comellas et al. (2021), Local mechanical stimuli shape tissue growth in vertebrate joint morphogenesis, preprint on bioRxv, doi:10.1101/2021.08.28.458034.
We process 3D image stacks showing axolotl elbows stained with click-it ready AHA and EdU molecules, which allow us to quantify humerus bone rudiment shape and cell proliferation, respectively. It is written as a step-by-step tutorial aimed at inexperienced users of Fiji and/or MATLAB. The scripts mentioned here are also provided and contain self-explanatory annotations of their contents as well as example input files to be able to run them.