Pinned Repositories
cagedopt
Microfluidics Imaging Rigs with Caged Optics
FluoroCellTrack
High-throughput droplet microfluidic devices with fluorescence detection systems provide several advantages over conventional end-point cytometric techniques due to their ability to isolate single cells and investigate complex intracellular dynamics. While there have been significant advances in the field of experimental droplet microfluidics, the development of complementary software tools has lagged. Existing quantification tools have limitations including interdependent hardware platforms or challenges analyzing a wide range of high-throughput droplet microfluidic data using a single algorithm. To address these issues, an all-in-one Python algorithm called FluoroCellTrack was developed and its wide-range utility was tested on three different applications including quantification of cellular response to drugs, droplet tracking, and intracellular fluorescence. The algorithm imports all images collected using bright field and fluorescence microscopy and analyzes them to extract useful information. Two parallel steps are performed where droplets are detected using a mathematical Circular Hough Transform (CHT) while single cells (or other contours) are detected by a series of steps defining respective color boundaries involving edge detection, dilation, and erosion. These feature detection steps are strengthened by segmentation and radius/area thresholding for precise detection and removal of false positives. Individually detected droplet and contour center maps are overlaid to obtain encapsulation information for further analyses. FluoroCellTrack demonstrates an average of a ~92-99% similarity with manual analysis and exhibits a significant reduction in analysis time of 30 min to analyze an entire cohort compared to 20 h required for manual quantification.
gramm
Gramm is a complete data visualization toolbox for Matlab. It provides an easy to use and high-level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.
Harvard_Pump
fluidic pump control
Homepage
matlab-schemer
Apply and save color schemes in MATLAB with ease.
PlotPub
Publication quality plot in MATLAB.
project-e-coli-sauna
A miniature sauna for happy E coli. A temperature controlled box with humidity logging made from an ItsyBitsy M4, DHT22 and an Aim TTi PSU with two heaters.
pydub
Manipulate audio with a simple and easy high level interface
the-craft-of-selfteaching
One has no future if one couldn't teach themself.
Jiaming-Zhang's Repositories
Jiaming-Zhang/cagedopt
Microfluidics Imaging Rigs with Caged Optics
Jiaming-Zhang/FluoroCellTrack
High-throughput droplet microfluidic devices with fluorescence detection systems provide several advantages over conventional end-point cytometric techniques due to their ability to isolate single cells and investigate complex intracellular dynamics. While there have been significant advances in the field of experimental droplet microfluidics, the development of complementary software tools has lagged. Existing quantification tools have limitations including interdependent hardware platforms or challenges analyzing a wide range of high-throughput droplet microfluidic data using a single algorithm. To address these issues, an all-in-one Python algorithm called FluoroCellTrack was developed and its wide-range utility was tested on three different applications including quantification of cellular response to drugs, droplet tracking, and intracellular fluorescence. The algorithm imports all images collected using bright field and fluorescence microscopy and analyzes them to extract useful information. Two parallel steps are performed where droplets are detected using a mathematical Circular Hough Transform (CHT) while single cells (or other contours) are detected by a series of steps defining respective color boundaries involving edge detection, dilation, and erosion. These feature detection steps are strengthened by segmentation and radius/area thresholding for precise detection and removal of false positives. Individually detected droplet and contour center maps are overlaid to obtain encapsulation information for further analyses. FluoroCellTrack demonstrates an average of a ~92-99% similarity with manual analysis and exhibits a significant reduction in analysis time of 30 min to analyze an entire cohort compared to 20 h required for manual quantification.
Jiaming-Zhang/gramm
Gramm is a complete data visualization toolbox for Matlab. It provides an easy to use and high-level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.
Jiaming-Zhang/Harvard_Pump
fluidic pump control
Jiaming-Zhang/Homepage
Jiaming-Zhang/matlab-schemer
Apply and save color schemes in MATLAB with ease.
Jiaming-Zhang/PlotPub
Publication quality plot in MATLAB.
Jiaming-Zhang/project-e-coli-sauna
A miniature sauna for happy E coli. A temperature controlled box with humidity logging made from an ItsyBitsy M4, DHT22 and an Aim TTi PSU with two heaters.
Jiaming-Zhang/pydub
Manipulate audio with a simple and easy high level interface
Jiaming-Zhang/the-craft-of-selfteaching
One has no future if one couldn't teach themself.