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binary-ivap

biosegment

BioSegment is a software stack to enable segmentation of microscopy data using machine learning models.

brainimmuneatlas

Overview of the scripts used to analyse the brainimmuneatlas data

cifconvert

cifconvert is a package built on the python-bioformats package that saves images and masks from the proprietary Amnis CIF-file format to an HDF5 file.

comp_cytometry

computational_pipeline_cvid

Code used to generate results for paper "A computational pipeline for the classification of CVID". This paper is submitted to Frontiers Immunology

computational_pipeline_euroflow_aml

computationalcytometry

Workshop computational cytometry

cytobright

Estimate Stain Index for single stained cytometry files.

cytof_covid19_study

R scripts to analyse the CYTOF data generated by the team of Frederik De Smet

cytonorm

R library to normalize cytometry data

cytonorm_figures

Scripts to replicate the figures reported in the CytofNorm publication.

cytonorm_note

R code to demonstrate the functionalities of CytoNorm2.0

dambi-hpc-guide

Basic and Advanced usage of High-Performance Computing in Bioinformatics

deeplearning_for_imagingflowcytometry

A framework around Tensorflow-Keras that makes it easy to train and evaluate any deep learning architecture on imaging flow cytometry data.

floremi

Submission to the FlowCAP IV challenge: Survival time prediction based on flow cytometry data

flowcytometryscripts

flowsom

Using self-organizing maps for visualization and interpretation of cytometry data

flowsom_protocol

R code to demonstrate the FlowSOM analysis pipeline.

flowsom_python

The complete FlowSOM package known from R, now available in Python!

flowsom_workshop

Example usage of the FlowSOM package

groupenc

Encoder with group loss for global structure preservation

harpy

hooktest

hydra_hpc_example

Hydra HPC example

ideas-to-zarr

Scripts for the conversion of data collected on Luminex imaging flow devices to a zarr file.

kiss_et_al_cellularimmunologyreview

R code to replicate the tSNE and FlowSOM figures

liechti_et_al_twinstudy

Code used to generate the results described in Liechti et al.

logo

dambi logo

marble-sorter-ui

Interface for the marble sorter