Microscopy Image Analysis
Deep learning and image analysis methods for biological microscopy data, including segmentation, classification, visualization, and annotation refinement.
Bioinformatics · Computational Biology · Research Software
Hi, I’m Sajjad Khawari.
I am an M.Sc. Bioinformatics student at Freie Universität Berlin. I work on reproducible bioinformatics software, computer vision models, and data analysis workflows for biological research.
My current interests include microscopy image analysis, genome analysis, annotation refinement, and practical research tools that can be used and extended by other scientists.
Current focus
Research interests
I enjoy projects where biological questions, data analysis, and software engineering meet. I care about tools that are not only technically correct, but also understandable and reproducible.
Genomics Workflows
Reproducible workflows for sequencing data, bacterial genome analysis, and comparative genomics with a focus on clear structure and automation.
Research Software
Practical Python and C++ tools for biological data analysis, with attention to usability, documentation, and reproducible results.
Selected work
Projects
A small selection of projects from my studies, research work, and personal GitHub repositories. I keep this list focused on projects that represent what I currently work on.
Ascaris Stage Segmentation
Deep learning pipeline for segmenting and classifying developmental stages of Ascaris suum embryos from microscopy images.
Open repository →Outbreak Detection for SARS-CoV-2
Analysis of SARS-CoV-2 sequencing data for outbreak detection and genomic epidemiology in a practical public health context.
Open repository →Bacterial Genome Analysis
Workflow for bacterial genome assembly, annotation, and downstream analysis with a focus on automation and reproducibility.
Open repository →Applied Sequence Analysis
Practical sequence analysis work covering common bioinformatics tasks, workflow structure, and Python-based data analysis.
Open repository →Machine Learning and AI in Life Sciences
Course-related machine learning projects for biological and biomedical data, including model development, evaluation, and interpretation.
Open repository →Bachelor Thesis
Implementation work around recursive run-length encoding and compressed FM-index structures, combining C++ programming and algorithmic bioinformatics.
Open repository →Technical profile
Languages, tools and methods
I use these tools across university projects, research work, and personal software projects.
Programming
Python
C++
R
Bash
HTML/CSS
Git
Linux
Data & Machine Learning
NumPy
Pandas
scikit-learn
PyTorch
OpenCV
Matplotlib
Jupyter
Bioinformatics
Snakemake
Biopython
Genome Assembly
Sequence Analysis
Image Analysis
Workflow Development
HPC
Nostra Omics
Small tools for practical bioinformatics
I also work on Nostra Omics, a small platform for documenting and sharing practical bioinformatics workflows and tools for labs and students.