software and Datasets

Cell Tracking

Single-cell analysis offers a level of discrete detection unobtainable with traditional batch-culture methods that provides highly informative data, particularly in heterogeneous populations. We have developed an open-source pipeline that combines machine learning (Fiji’s Trainable Weka Segmentation) and custom Python scripts to identify (segment) and track cells in any series of 16-bit tiff images. The pipeline analyzes cell size, location, movement, division and fluorescence with respect to time and cell lineage.

The pipeline is available on GitHub: Link

Demo videos and sample datasets: https://osf.io/75avy/
Scripts: https://github.com/hdeter/CellTracking

Video_S2_A_xy5-8.mp4

data_Test_xy5_full_stacked.mp4

V1-microscope-video.mp4

V5-Lineages_short.avi

V3-segmentation.mp4

Tracking 1,000s of cells

Get cell size, location, division, fluorescence, etc.
Human readable datafiles (csv)
Videos

Colony Counting

The Colony Counting software is typically used to count the number of colonies on a standard Petri dish. Scripts that utilize the Weka Segmentation Tool in ImageJ to train and classify images via machine learning. Images can be cropped before classification. Classified images are then counted and a csv file containing the final counts is generated. These scripts were designed to count agar plates after scanning images on a flatbed scanner.
Scripts: https://github.com/hdeter/CountColonies

PythonWorkshop (for beginners)

A simple online workshop to train beginners (geared towards biologist) in Python coding
Scripts: https://github.com/hdeter/PythonWorkshop

RNA-sequencing data

Deter, H. S., T. Hossain and N. C. Butzin (2020). "Antibiotic tolerance is associated with a broad and complex transcriptional response in E. coli." bioRxiv. doi: https://doi.org/10.1101/2020.08.27.270272
- Data is available in NCBI GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156896

Disclaimer: This is website is maintained by Dr. Nicholas C. Butzin. Information presented here does not represent official views or opinions of South Dakota State University or any other association that Dr. Butzin is connected with.

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