Discover labsyspharm/quantification Open Source project

Multiple-choice microscopy pipeline

122

mcmicro

Nextflow

104

scimap

Spatial Single-Cell Analysis Toolkit

Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

minerva-story

minerva_analysis

An Interactive Image Segmentation Filter for Multiplex Microscopy

cylinter

Piecewise alignment for layers of mosaics

palom

visinity

Tool to create images and configuration files for Minerva-Story

smallmoleculesuite-old

minerva-author

Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.

ome-tiff-pyramid-tools

Scope2Screen is an open-source web-application for focus+context exploration and annotation of whole-slide, high-plex, tissue images.

scope2screen

Resources for Drug Repurposing In Alzheimer's Disease (DRIAD) work

DRIADrc

CRC_atlas_2022

orion-crc

Drug Repurposing in Alzheimer's Disease

DRIAD

basic-illumination

ImageJ BaSiC shading correction for use with Ashlar

Inference of cell states using Naive Bayes

naivestates

smallmoleculesuite

cluequery

An R interface to the Connectivity Map API at clue.io

redseapy

API for performing all kinds of cheminformatics task, like fingerprinting and chemical similarity computations

lsp-cheminformatics

Kinase-compound affinity prediction based on structures

KinCo

minerva-browser

Supplementary Material for the MARM2.0 model

marm2-supplement

Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views.

minerva-author-ui

Efficient structure for storing and comparing Morgan fingerprints

morgancpp

dubportal

An integrative resource for deubiquitinating enzymes (DUBs) served at https://labsyspharm.github.io/dubportal

Supplemental code and model files for the MARM1 model publication, Gerosa et al.

marm1-supplement

Harvard Tissue Atlas website

harvardtissueatlas

SCSS

PanFab-PAPR-2021

Greater Boston Pandemic Fabrication Team Powered Air-Purifying Respirator (PanFab PAPR)

C++

UnMICST-info

cycif.org GitHub Pages Website

cycif.org

Convert a Leica .SCN file to OME-TIFF format

scn2ometiff

minerva-lib-python

Minerva Python Library

Repository for OMERO related scripts

OMERO_scripts

vae-paper

Create thumbnails of cells in a given image.

cellcutter

Guide for aligning deep RNAseq and Digital Gene Expression (DGE) reads using bcbio.

rnaseq

CSS

minerva-cloud

Minerva Cloud is a novel cloud-native (AWS) platform for high-dimensional microscopy image storage, management, and visualization.

Scripts for maintaining and processing Small Molecule Suite data.

sms-maintenance

selectivity_comparisons

enrichr.db

Data package providing gene sets from Enrichr in R

cd73_coy_spatialcorrelation

Web app for Drug Repurposing in Alzheimer's Disease

driad-website

lincs_proteomics_data_descriptor

This repository includes code used to process and visualize datasets that feature in the LINCS proteomics data descriptor

dark-kinome-old

aws-tools

General purpose scripts for managing our AWS usage

Shell

palmer-plana-2020

Mathematica

lymphonet_2023

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

Ilastik segmentation module for mcmicro

digipath_ml

mcmicro-ilastik

Ludwig Tumor Atlas website

ludwigtumoratlas.org

SCSS

pamsig

Partitioning Around Medoids (PAM) and generation of cluster SIGnatures

mcmicro-scanpy

An MCMICRO module implementation of scanpy for clustering cells

A site describing LSP compounds served at https://labsyspharm.github.io/lspci/

lspci

bfextractor

Scripts and data for NPJ Breast Cancer 2023 (Guerriero-Lin-Santagata)

npjbcancer2023

cylinter-paper

Interactive dashboard showing DNA correlation coefficient as indicator of tissue integrity at single cell level

kinome-website

tissue_integrity_dashboard

Minerva Command Line Interface

minerva-cli

Bio-Formats Directory Scanner

bfscanner

Java

minerva-cloud-ui

Minerva Cloud is a novel cloud-based (AWS) software for high-dimensional image management, storage and visualization.

gater