Data Analysis

Free* software

ImageJ

• https://imagej.nih.gov/ij/
• 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 https://fiji.sc/ “Ready to go” bundle of ImageJ plugins focused on life sciences applications with friendly user interface

Cell profiler

• https://cellprofiler.org/releases/
• User-friendly MATLAB-based tool to analyze and batch-process cells with a simple “point and click” approach, and the options to assemble modules into a pipeline.
• Key features: image loading, homogenization of the illumination, object identification and object measurement.
• Workshop: https://www.youtube.com/watch?v=OgyfbJOMr70

QuPath

• https://qupath.github.io/
• Free, open-source desktop application designed by Bankhead (Queen’s Univ.) for whole slide image analysis, biomarker analysis, IHC quantification, and tumor analysis on H&E
• Workshop: qupath for fiji users https://www.youtube.com/watch?v=xW2Ya205nvo

Orbit

• https://www.orbit.bio/
• 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.

Bioconductor-R

• https://bioconductor.org/packages/release/bioc/html/EBImage.html
• 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 **

• https://www.arivis.com/
• 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

Imaris

• https://imaris.oxinst.com/big-data  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.

Napari

• https://napari.org/stable/
• Python image viewer for multi-dimensional large image analysis (you can browse, annotate, and analyze them)

Cellpose

• https://www.cellpose.org/
• Generalist algorithm for cell segmentation via artificial intelligence algorithms, can be tested online

GliaMorph

• Modular image analysis toolkit for glial cell morphology quantification, implemented as Fiji Macros for modular application
• Applications: Measure astrocyte length…
• https://github.com/ElisabethKugler/GliaMorph
• https://www.biorxiv.org/content/10.1101/2022.05.05.490765v1

• Ilastik
  • https://www.ilastik.org/download.html
  • User-friendly open-source tool for segmentation and classification of images (2D, 3D, and 4D)
  • Applications include cell segmentation, classification, tracking, and counting
• Icy
  • http://icy.bioimageanalysis.org/download/
  • 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

• http://icy.bioimageanalysis.org/download/
• 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

Amira

• https://en.wikipedia.org/wiki/Amira_(software)
• Developed by Thermo Scientific, it is a comprehensive tool for visualization and analysis of 2D-5D optical, CT, and MRI images

Arivis 4D **

• https://www.arivis.com/
• 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

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 360.2.0.pl.1)
• Outputs: raw Bruker data (2dseq), nifty (.nii), DICOM (.dcm)

MATLAB

• Free MATLAB academic license, for Northeastern students*
• User-developed codes are required for image analysis
• Please contact CILS if you need assistance with the development of MATLAB algorithms for MRI data analysis

Segment Mediviso 

• • https://medviso.com/segment/
  • 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.
    

Python

• • • https://www.python.org/about/
    • User-developed codes are required for image analysis. Open access resources in
      • https://www.frontiersin.org/articles/10.3389/fninf.2020.00024/full
      • https://github.com/topics/preclinical-imaging
      • https://www.youtube.com/watch?v=gMuxB18Cr0o (video tutorial)

    3D Slicer

    • https://slicer.org/
    • Enables DICOM, nifti (and others) visualization of images as well as post-processing. Some features include: image segmentation, volume rendering, feature extraction, image registration, image stitching… Multiple module can be developed or imported from the cloud for more advanced analysis.
    • More information for MRI analysis with 3D slicer is included in http://dmri.slicer.org/

     

    ImageJ

    • https://imagej.nih.gov/ij/
    • 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…
    • MRI analysis can be done by importing MRI plugins
    • Note: ImageJ does not handle Bruker raw data format (2dseq, fid) and requires additional steps https://imagej.nih.gov/ij/plugins/mri-file-manager/index.html

Paid software

Amira

• • https://en.wikipedia.org/wiki/Amira_(software) developed by Thermo Scientific, it is a comprehensive tool for visualization and analysis of 2D-5D optical, CT, and MRI images

• With Visualsonics users get access to Vevolab https://www.visualsonics.com/product/software/vevo-lab
  • Cardiovascular analysis – key features: Automatic functional and structural LV analysis, perfusion kinetics quantitative assessment, global and regional wall LV assessment, wall thickness evaluation. Other packages are especially designed for oncology, neurobiology, and molecular imaging applications.
  • Additional platform for data management and handling, compatible with the Vevolab software https://www.visualsonics.com/product/software/visualsonics-ipacs
• Resources
  • Comprehensive review of techniques and applications https://www.frontiersin.org/articles/10.3389/fphy.2020.00124/full

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.  

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.