Pinned Repositories
2021_Doddihal
Fiji processing macros associated with Doddihal et al.
2023_Gupta
Code associated with the submitted publication of Ayantika Sen Gupta, for 1) Finding pairs of peaks in CenpA, 2) Cropping and aligning them, 3) Analyzing the spatial intensity distribution.
2024_Primate_rDNA
dask-slurm-tutorial
Gerton_Robertsonian_2024
git_test
H3p_Quantification
A common analysis pipeline for finding spots and worms from low resolution spinning disk data. This is interactive: with outlier elimination easily screened for by clicking on points in extraneous points in plotly, visualizing the corresponding image in napari, and allowing one to remove that point from further analysis.
InSituQuantification_Cellpose
Combines an ImageJ friendly version of cellpose (see other repository), napari and plotly to perform per nucleus in situ quantification and colocalization.
smc-macros
Complete suite of ImageJ/Fiji macros written by Sean McKinney for performing various image processing tasks at the Stowers Institute.
SpatialTranscriptomics
Code for troubleshooting, analyzing and displaying SlideSeq data
jouyun's Repositories
jouyun/smc-macros
Complete suite of ImageJ/Fiji macros written by Sean McKinney for performing various image processing tasks at the Stowers Institute.
jouyun/SpatialTranscriptomics
Code for troubleshooting, analyzing and displaying SlideSeq data
jouyun/2021_Doddihal
Fiji processing macros associated with Doddihal et al.
jouyun/2023_Gupta
Code associated with the submitted publication of Ayantika Sen Gupta, for 1) Finding pairs of peaks in CenpA, 2) Cropping and aligning them, 3) Analyzing the spatial intensity distribution.
jouyun/2024_Primate_rDNA
jouyun/dask-slurm-tutorial
jouyun/Gerton_Robertsonian_2024
jouyun/git_test
jouyun/H3p_Quantification
A common analysis pipeline for finding spots and worms from low resolution spinning disk data. This is interactive: with outlier elimination easily screened for by clicking on points in extraneous points in plotly, visualizing the corresponding image in napari, and allowing one to remove that point from further analysis.
jouyun/InSituQuantification_Cellpose
Combines an ImageJ friendly version of cellpose (see other repository), napari and plotly to perform per nucleus in situ quantification and colocalization.
jouyun/smc-plugins
Java code for Sean McKinney's ImageJ plugins from the Stowers Institute.
jouyun/ip_python
jouyun/Mann_2023
jouyun/napari-cellposetrainer
jouyun/napari-cziviewer
jouyun/napari-vsiexporter
jouyun/napari-xenium
jouyun/pub-2020elife
Fiji macros associated with processing data from Chen et al., eLife 2020.
jouyun/python-hammy
jouyun/python_introDS_course
Intro to python for data science using Pandas and Jupyter Notebooks
jouyun/pytorch
Unets, auto-encoder, classifier for 2D/3D image analysis
jouyun/Rohner_2025_Ovary
jouyun/scikit-image
Image processing in Python
jouyun/Tensorflow
Older code for Unets, auto-encoders, convonets in Tensorflow. Includes original code for processing RNA Fish spots and segmenting EM Nucleii.