tp81 Goto Github PK

abcd-dicom2bids

For selectively downloading ABCD data QC'ed as good by the DAIC, converting it to BIDS standard input data, selecting the best pair of spin echo field maps, and correcting the sidecar JSON files to meet BIDS Validator spec.

analysis-workflow-20190502

Analysis workflow May 2nd 2019

bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

cellfinder-brainreg-docker

cellprofiler

An open-source application for biological image analysis

cellprofiler-docker

Dockerized CellProfiler

clij2-stardist-plugin

Run StarDist as a CLIJ2 function

clijx-assistant-stardist

consul

Consul is a tool for service discovery, monitoring and configuration.

cytopacq

Dockerized version of Cytopacq

datalad-first-test

some default

distributed-cellprofiler

Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.

dockerfiles

Some Dockerfiles

ep-analysis-matlab

Electro-physiology analysis software written in MATLAB

gpt4all-docker

holly

HOLLy - A neural network project to determine 3D structure from 2D SMLM images.

huygens-scripts

Various huygens TCL scripts

imariswriter

lemos-qupath-2021

methodsj

Helps to write the material and methods section of a scientific article, by automatically generating a description of the imaging parameters.

midb-open-data-docs

Documentation for the Masonic Institute for the Developing Brain (MIDB) Open Data Initiative

msi-fatchecker-round2

some default

neisch-dynein-2021

Code associated with manuscript by Neisch et al.

nikon-biostation-utils

Stitching for the Nikon Biostation.

nmf-ml

Multi-layer non-negative matrix factorization MATLAB implementation.

omero-scripts

Some OMERO scripts

omero-user-scripts

Plugins for OMERO

openmicroscopy

OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded by private and public research grants, OME has been a major force on the international microscopy stage since 2000.

ostrander-2020

Scripts related to the manuscript

peri

Parameter Extraction from Reconstructing Images