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analysis-on-membrane-labeled-cell

Distinguish cells labeled with membrane structure and analyze the volume and intensity in each cell.

automatic-billing-system

To integrate the charging from the optical microscope, the advanced optical microscope and the electronic microscope, I designed this system to automatically sort bills to each PI and generate monthly and yearly data.

batch-assay-in-oil-red-stain

This Fiji macro is designed to automatically measure the oil red occupation and intensity in tissues from tif files collected in a folder.

bioimage-analysis-workshop-23-24

All materials for bioimage analysis workshop at Kyoto and Taipei, Dec 2023 and Jan 2024

cell-classification-from-dual-fluorescence-labels

The nucleus is identified by a Weka-trained model. Then the ROI generated by the identified nucleus is applied to both green and red mask to classify cells.

cell-grouping

The red fluorescence labeled cells are distributed in a cluster manner. These tools are used to define the cluster code for each interested nucleus.

contact-angle-of-vesicles

The tool in this repository is designed to analyze the contact angle of neighboring subcellular vesicles captured by fluorescence microsocopes including widefield, confocal and super-resolution images.

embl-ebi-imaging-course-05-2023

green-intensity-over-total-cell-no

This is an automatic tool to quantify the green fluorescence signal over the total cell number from high content images.

mitosis-phase-analysis

A cell cycle occurs as a cell divides. The somatic cell leaves interphase, undergoes mitosis and eventually gives out two daughter cells. Mitosis is composed by a series of events including prophase, metaphase, anaphase and telophase. Each phase is featured by DNA condensation, chromosomes lining up along the metaphase plate, segregation of duplicated chromosomes, and DNA decondensation, respectively. Here I offered a tool generated on Fiji plateform to identify the start of each phase and calculate the duration of them.

myotome-volume-nucleus-count-and-color-analysis

The tools in this repository are designed to analyze the confocal images of zebrafish myotome whose membrane is labeled by the multicolor cell barcode (ref1). Three types of analysis done by five scripts are included in this repository. The first application is used to process the zebrafish myotome image before 3D volume quantification. Second, a stack image with the center of each nucleus is built. Therefore, the nucleus number can be counted along with myofibers. Third, the unique color of the multicolor labeling was extracted iteratively from images which constitute a single myotome. At the end, the python tool is used to project the identified color to a 3D plot with gray value RGB as axes to draw the representative result image.

neubias_analystschool2019

NEUBIAS Bioimage Analyst School 2019

neubias_analystschool2020

omero-guide-python