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align_pipeline

The alignment pipeline for Shield signal detection

araw2tif

A utility for backing up .raw files to .tif

axon-centerline-detection

beegfsmonitor

A UI for displaying telemetry data from beegfs-mon

blockfs

A 3D block file storage system optimized for multiprocessing

bmtrap_2021

celltool

Command-line tools for statistical analysis of shapes, particularly cell shapes from micrographs.

ceph-smartctl

Uses smartctl to check for failed CEPH drives

chunglab_dz

Blockfs to deep zoom translator for the chunglab website.

dandi-io

Remote access to dandisets

data-processing-tools

Various data processing tools developed by Nick D. as pipeline practice

docker_simpleelastix

Dockerfile for building the superbuild image of simpleelastix

eflash_2018

frangi3d

Computes vesselness scores for 3-dimensional images.

gwdt

Grey-weighted distance transform

leica2tif

A quick command-line tool to convert Leica files to TIF.

mp_shared_memory

A shared-memory wrapper backwards compatible with Python < 3.8

nuggt

NeUroGlancer Ground Truth - annotate cell centers

pacqproc

Post-acquisition processing pipelines for light-sheet microscopy

pavlidis

The Pavlidis algorithm for contour tracing

phathom

Phenotypic analysis of brain tissue at single-cell resolution

pmetsurf

Parametric surfaces using splines

precomputed-tif

A simple utility to generate a precomputed data source as TIF files along with a simple HTTP server of those files.

psviewer

Pre-stitched viewer of light sheet images

pyina

MPI parallel map and cluster scheduling

pystripe

An image processing package for removing streaks from SPIM images

pystripe-ui

User interface for crafting scripts for running PyStripe

rigid-rotate

A React web-app for rotating two volumes into rough alignment

rotate2d

A quick GUI for rotating ZARR files in 2D.

scout

Multiscale hyperdimensional phentypic analysis of organoids