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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.

ip_python

mann_2023

napari-cellposetrainer

napari-cziviewer

napari-vsiexporter

napari-xenium

pub-2020elife

Fiji macros associated with processing data from Chen et al., eLife 2020.

python-hammy

python_introds_course

Intro to python for data science using Pandas and Jupyter Notebooks

pytorch

Unets, auto-encoder, classifier for 2D/3D image analysis

scikit-image

Image processing in Python

smc-macros

Complete suite of ImageJ/Fiji macros written by Sean McKinney for performing various image processing tasks at the Stowers Institute.

smc-plugins

Java code for Sean McKinney's ImageJ plugins from the Stowers Institute.

spatialtranscriptomics

Code for troubleshooting, analyzing and displaying SlideSeq data

tensorflow

Older code for Unets, auto-encoders, convonets in Tensorflow. Includes original code for processing RNA Fish spots and segmenting EM Nucleii.