Data Analysis

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Image Analysis Resources

Do you know any additional resources or have any comments regarding the ones listed? Please let us know!

1. Flow cytometry


Free* Software

Flowing Software


WinMDI “Windows Multiple Document Interface”


  • Microsoft environment flow cytometry analysis software with basic analysis features: statistics, dot plot, histogram…


Frank Battye

  • Free, open source software includes:
    • Cellular symphony: each cell represents a musical note dependent on its properties, to develop an audio representation of flow cytometry data
    • Hackit: serves to clip stream of cells that may have affected a file when a file is suspected to be corrupted (e.g., from cell carryover)
    • De-identifier: to anonymize data by removing patient identification



  • User friendly and open-source tool for flow cytometry data analysis & visualization
  • Runs using Matlab or Octave

Red matter


Paid Software:


FCS Express



  • User-friendly software with 3D graphics, sticky regions and magic contour functionalities, cen-se and t-SNE dimensionality reduction capabilities
  • Applications: color gating, quantitative analysis, rare-event analysis, immune-phenotyping…

2. Microscopy

Free* software


  • Free, Java-based image processing tool developed as a collaboration between NIH and Univ. Wisconsin for basic image visualization and analysis, including data scaling, segmentation, and 3D volume rendering…
  • Fiji “Ready to go” bundle of ImageJ plugins focused on life sciences applications with friendly user interface

Cell profiler



  • Free, open-source tool for whole slide image quantification. It accepts images from Omero (Open Microscopy environment image server). Key features include object/cell segmentation, object classification, and implementation of machine learning algorithms.


  • Free EBimage software for image processing and analysis to segment cells and extract quantitative cellular descriptors
  • Built in R programming language, users with knowledge in R can develop advanced methods for visualization, signal processing, statistical modeling, and machine learning implementations.

Arivis 4D **

  • Free for CILS users**
  • Microscopy image data visualization platform to improve data accessibility with capabilities for advanced workflows: high content screening, image annotation, and remote image analysis. CILS users have access
  • Highlighted features: segmentation tools, and ability to generate movies from 3D datasets by importing keyframes


  •  3D and 4D Real-Time Interactive Data visualization, analysis, stitching and deconvolution platform
  • Imaris is not free, but Imaris Viewer is a free 3D/4D microscopy image viewer for viewing raw images as well as those analyzed within Imaris.


  • Python image viewer for multi-dimensional large image analysis (you can browse, annotate, and analyze them)


  • Generalist algorithm for cell segmentation via artificial intelligence algorithms, can be tested online


  • Ilastik
    • User-friendly open-source tool for segmentation and classification of images (2D, 3D, and 4D)
    • Applications include cell segmentation, classification, tracking, and counting
  • Icy
    • Open-source tool developed by France-BioImaging and Institute Pasteur for visualization, annotation, and quantification of bioimaging data. It enables the development of algorithms for more advance examinations.

Aqua software

  • For quantification of heterogeneous, propagative, and/or irregular fluorescence dynamics (ref), specifically to analyze intensity fluctuations of individual pixels and therefore evaluate temporal nanosensor response calculation in addition to quantifying spatial propagation of the fluorescent signal across the ganglion. Clark Lab/Monaghan Lab in PNAS



Paid software


Arivis 4D **

  • Free for CILS users**
  • Microscopy image data visualization platform to improve data accessibility with capabilities for advanced workflows: high content screening, image annotation, and remote image analysis. CILS users have access
  • Highlighted features: segmentation tools, and ability to generate movies from 3D datasets by importing keyframes

3. MRI

Free* software

ParaVision software

  • Included in the MRI scanner, free for CILS users*, developed by Bruker
  • Features:
    • Image analysis and calculation of parameter maps: T1, T2, proton density, maximum/minimum intensity projections, ADC, diffusion tensor,
    • Image handling and post-processing: stitching, fusion, 3D volume rendering…
  • Valid inputs: images acquired with the same Paravision version or older (currently installed in the scanner are: ParaVision 360.1.1 and Paravision
  • Outputs: raw Bruker data (2dseq), nifty (.nii), DICOM (.dcm)


Segment Mediviso 

    • Free for research purposes*, including analysis of MRI, CT, and SPECT cardiac images.
    • Key features: left ventricle and right ventricle volumetric analysis, flow characterization, relaxometry quantification (including T1, T2, T2*, and ECV analysis), 3D measurements, fusion methods, ROI and signal intensity analysis, etc.


Paid software


4. Ultrasounds

5. Data Management

5.1 Data Storage  

The Core Facility does not guarantee the safety or storage of any data saved on a workstation or OMERO cloud storage. 

It is the user’s responsibility to make a permanent copy of his or her data upon completion of a session. Workstations  have temporary storage available to users to save data during the session; however, upon completion of a session, data must be transferred off the workstation using one of the methods below:  

Cloud storage: users may use any cloud-based storage service available to them. Each workstation is connected to the internet for high-speed data transfer.  

OMERO: internal users may use OMERO, a cloud storage service provided by the university for temporary storage. Users will need to setup an account before data may be transferred. Core Facility staff can assist users with how to setup an account and transfer their data to OMERO.  

Due to the threat of virus transfer, users are prohibited from connecting a USB drive or other portable storage device to any workstation. Download of programs or files to a workstation is prohibited.  

6. Acknowledgement

Please acknowledge the CILS Core Facility and Northeastern University in any publication or grant application where its instruments, knowledge/expertise or data helped support research activity. We suggest the following text in the acknowledgements section of your paper: “We thank the Institute for Chemical Imaging of Living Systems (RRID:SCR_022681) at Northeastern University for consultation and imaging support”.  

The CILS Core Facility staff would love to hear about any grant applications or papers accepted for publication.   

Our facility

Interdisciplinary Science and Engineering Complex

ISEC 080, 805 Columbus Ave, Boston, MA, 02115


Mild repetitive TBI reduces brain-derived neurotrophic factor (BDNF) in the substantia nigra and hippocampus: A preclinical model for testing BDNF-targeted therapeutics
Wooden Steps to Shallow Depths: A New Bathymodiolin Mussel, Vadumodiolus teredinicola, Inhabits Shipworm Burrows in an Ancient Submarine Forest
Milk Exosomes Anchored with Hydrophilic and Zwitterionic Motifs Enhance Mucus Permeability for Applications in Oral Gene Delivery
Engineered Bacteria Titrate Hydrogen Sulfide and Induce Concentration-Dependent Effects on Host in a Gut Microphysiological System
Endothelial Glycocalyx Sensitivity to Chemical and Mechanical Sub-Endothelial Substrate Properties
Controlling Pericellular Oxygen Tension in Cell Culture Reveals Distinct Breast Cancer Responses to Low Oxygen Tensions
Hypoxia-Inducing Cryogels Uncover Key Cancer-Immune Cell Interactions in An Oxygen-Deficient Tumor Microenvironment
Direct Differentiation of Human Pluripotent Stem Cells into Vascular Network along with Supporting Mural Cells


Bioengineered Perfused Human Brain Microvascular Networks Enhance Neural Progenitor Cell Survival, Neurogenesis, And Maturation
Pten, Pi3K and PtdIns(3,4,5)P3 Dynamics Modulate Pulsatile Actin Branching in Drosophila Retina Morphogenesis
Medioapical Contractile Pulses Coordinated between Cells Regulate Drosophila Eye Morphogenesis
Cationic Carrier Mediated Delivery of Anionic Contrast Agents in Low Doses Enable Enhanced Computed Tomography Imaging of Cartilage for Early Osteoarthritis Diagnosis
Sox17 Mediates Adult Arterial Endothelial Cell Response to Hemodynamics
Cold Exposure Impairs Extracellular Vesicle Swarm–Mediated Nasal Antiviral Immunity
Lineage-Mismatched Mitochondrial Replacement in an Inducible Mitochondrial Depletion Model Effectively Restores the Original Proteomic Landscape of Recipient Cells
Exploring Functional Protein Covariation across Single Cells Using nPOP
Transport of Symbiont-Encoded Cellulases from the Gill to the Gut of Shipworms via the Enigmatic Ducts of Deshayes: A 174-Year Mystery Solved
Click Chemistry-Enabled Conjugation Strategy for Producing Dibenzodiazepinone-Type Fluorescent Probes To Target M2 Acetylcholine Receptors
Developing a Transwell Millifluidic Device for Studying Blood-Brain Barrier Endothelium
Diosmin and Its Glycocalyx Restorative and Anti‐Inflammatory Effects on Injured Blood Vessels
pH-Responsive i-motif-Conjugated Nanoparticles for MRI Analysis
Hybridization Chain Reaction Fluorescence In Situ Hybridization (HCR-FISH) in Ambystoma mexicanum Tissue
Intra-Articular Kinetics of a Cartilage Targeting Cationic PEGylated Protein for Applications in Drug Delivery
Charge-Based Drug Delivery to Cartilage: Hydrophobic and not Electrostatic Interactions are the Dominant Cause of Competitive Binding of Cationic Carriers in Synovial fluid
In vitro Testbed Platform for Evaluating Small Volume Contrast Agents via Magnetic Resonance Imaging
Usability of Deep Learning Pipelines for 3D Nuclei Identification with Stardist and Cellpose
A Long-Circulating Vector for Aptamers Based upon Polyphosphodiester-Backboned Molecular Brushes
Hypoxia Inhibits the Cardiac IK1 Current through SUMO Targeting Kir2.1 Activation by PIP2
Denoising Multiplexed Microscopy Images in N-Dimensional Spectral Space
Cationic Peptide Carriers Enable Long Term Delivery of Insulin-Like Growth Factor-1 to Suppress Osteoarthritis-Induced Matrix Degradation
Increasing the Throughput of Sensitive Proteomics by plexDIA
Targeting Oncogenic KRAS with Molecular Brush-Conjugated Antisense Oligonucleotides


Local Mechanical Stimuli Correlate with Tissue Growth in Axolotl Salamander Joint Morphogenesis
Maximizing TLR9 Activation in Cancer Immunotherapy with Dual-Adjuvanted Spherical Nucleic Acids
Single-Dose Intra-Cartilage Delivery of Kartogenin Using a Cationic Multi-Arm Avidin Nanocarrier Suppresses Cytokine-Induced Osteoarthritis-Related Catabolism
Regenerating Axolotl Retinas Regrow Diverse Cell Types with Modulation by Notch Signaling and Reconnect to the Brain
Wnt Signaling Coordinates the Expression of Limb Patterning Genes During Axolotl Forelimb Development and Regeneration
A Constitutively Expressed Fluorescence Ubiquitination-Based Cell Cycle Indicator (FUCCI) in Axolotls for Studying Tissue Regeneration
Development of Fluorescently Labeled, Functional Type I Collagen Molecules
Interstitial Flow Enhances the Formation, Connectivity, and Function of 3D Brain Microvascular Networks Generated within a Microfluidic Device
Regeneration and Assessment of the Endothelial Glycocalyx To Address Cardiovascular Disease
Mild Repetitive Head Impacts Alter Perivascular Flow in the Midbrain Dopaminergic System in Awake Rats
Quantitative Imaging of Blood-Brain Barrier Permeability Following Repetitive Mild Head Impacts
High-Throughput Microfluidic 3D Biomimetic Model Enabling Quantitative Description of the Human Breast Tumor Microenvironment
Injectable Lignin-co-Gelatin Cryogels with Antioxidant and Antibacterial Properties for Biomedical Applications
Mechanical Causation of Biological Structure: Productive Pulls Produce Persistent Filaments in a Human Fibroblast Model of Matrix Development
Bottlebrush Polymer-Conjugated Melittin Exhibits Enhanced Antitumor Activity and Better Safety Profile
Two-Photon Peak Molecular Brightness Spectra Reveal Long-Wavelength Enhancements of Multiplexed Imaging Depth and Photostability


Stiffening of the Extracellular Matrix is a Sufficient Condition for Airway Hyperreactivity
Biomaterials and Oxygen Join Forces to Shape the Immune Response and Boost COVID-19 Vaccines
Imaging in vivo Acetylcholine Release in the Peripheral Nervous System with a Fluorescent Nanosensor
A DNA-Based MRI Contrast Agent for Quantitative pH Measurement
Confocal Imaging Capacity on a Widefield Microscope Using a Spatial Light Modulator
Lung Injury in Axolotl Salamanders Induces an Organ‐Wide Proliferation Response
3D Visualization of Macromolecule Synthesis
Self-Assembled DNA–PEG Bottlebrushes Enhance Antisense Activity and Pharmacokinetics of Oligonucleotides


High-Power Light-Emitting Diode Array Design and Assembly for Practical Photodynamic Therapy Research
Engineering Bacillus subtilis as a Versatile and Stable Platform for Production of Nanobodies
Optical Nanosensors for in vivo Physiological Chloride Detection for Monitoring Cystic Fibrosis Treatment
Site‐Specific Bioconjugation and Convergent Click Chemistry Enhances Antibody–Chromophore Conjugate Binding Efficiency
Real-Time Particle-by-Particle Detection of Erythrocyte-Camouflaged Microsensor with Extended Circulation Time in the Bloodstream
Multichannel Correlation Improves the Noise Tolerance of Real-Time Hyperspectral Microimage Mosaicking