Community Bonding II

Hi!

Further updates on the work:
1. I have posted the article titled A Beginner's Guide to Spatial Processes package of SBML Version 3 Core 2 on Medium. 
Link: https://medium.com/@me1999bh/a-beginners-guide-to-spatial-processes-package-of-sbml-version-3-core-2-2eba4babca11?source=friends_link&sk=cd36b695ab5dd644795bbc279bfd8c62 

2. An appropriate dataset of mouse neuroblastoma cells was found and shared by my mentor, Yuta Tokuoka. This dataset consists of wide-field epifluorescent images of cultured neurons with both cytoplasmic (phalloidin) and nuclear stains (DAPI) and a set of manual segmentations of neuronal and nuclear boundaries that can be used as benchmarking data sets for the development of segmentation algorithms.

Featured project: Autosegmentation of cultured neurons

Link: http://flagella.crbs.ucsd.edu/images/CCDB_6843

A typical cellular image from the dataset

Segmented mask corresponding to the image shown above

The dataset for this project requires images of single cells along with their segmentation. So, the only work left was to crop individual cells and group them together. So far, I have collected 600 images, each of dimensions 188 X 140 pixels. 

A typical single-cell image and corresponding segmented mask

3. I was able to build the XitoSBML code and run it on the Eclipse IDE 2020-03R for Java Developers. In this endeavor, I was helped by my mentors Kaito Ii and Akira Funahashi.
As a first step, the source code needs to be cloned.
% git clone https://github.com/spatialsimulator/XitoSBML.git 
Further steps are:
1. Import XitoSBML as a Maven project in Eclipse IDE.
2. Right-click the XitoSBML project.
3. Select 'Maven' --> "Update project".

Running MainImgSpatial.java

Till the next time

Au revoir!