Myofiber reconstruction at micron scale reveals longitudinal bands in heart ventricular walls

Drisya Dileep, Tabish A. Syed, Tyler F. W. Sloan, Perundurai S. Dhandapany, Kaleem Siddiqi, Minhajuddin Sirajuddin

Submitted 2022 bioRxiv DOI: 10.1101/2022.05.12.491149

I built a Blender-Python module to interface with 3D microscopy and vector field data arrays. The glyphs and streamlines were used in 3D renders in the figures and in supplemental videos.

Publications

Organizing Principles of Astrocytic Nanoarchitecture in the Mouse Cerebral Cortex.

Christopher K. Salmon, Tabish A. Syed, J. Benjamin Kacerovsky, Nensi Alivodej, Alexandra L. Schober, Michael T. Pratte, Michael P. Rosen, Miranda Green, Adario DasGupta, Hojatollah Vali, Craig A. Mandato, Kaleem Siddiqi, Keith K. Murai

Submitted 2022 bioRxiv DOI: 10.1101/2021.11.05.467391

I built a Blender-Python module to combine 3D reconstructions, precomputed paths and tabular data into user-friendly Blender models. Static renders in the paper were made from these models. I also composed a 4:30 "hype video" to accompany the paper and visually explain some of the geometric analysis methods.

Usiigaci: Instance-aware cell tracking in stain-free phase contrast microscopy enabled by machine learning

Tsai HF, Gajdac, J.Sloan TF, Rarese A, Shen AQ

2019 SoftwareX DOI: 10.1016/j.softx.2019.02.007

I built a Jupyter-Python notebook to perform cell migration calculations and produce automated plot outputs from the machine learning module.

Integration of shallow gradients of shh and netrin-1 guides commissural axons.

Sloan TF, Qasaimeh MA, Juncker D, Yam PT, Charron F

2015 PLoS Biol DOI: 10.1371/journal.pbio.1002119

This paper was my thesis work. I developped a microfluidic gradient assay, and performed cell migration experiments on neurons. I wrote analysis software to compute axon migration and gradient measurements, and produced all of the graphics from the article.

Quorumetrix

Data Driven Design