Image Analysis

Image Analysis

The Image Analysis unit is a provider of state-of-the-art image processing and data analysis services. Our team of experts leverages cutting-edge technologies and methodologies to extract valuable insights from diverse imaging data sources. With a focus on accuracy and efficiency, we deliver tailored solutions for the academy and the industry.

Our services include:

  • Image enhancement
  • Noise reduction
  • Image segmentation
  • Object detection and recognition
  • Feature extraction
  • Quantitative analysis
  • Image registration
  • Image fusion
  • Stand-alone image processing tools
  • Visualization
  • Partial or full participation in research, including advisory and supervisory roles

By employing advanced algorithms accompanied by machine and deep learning techniques, we provide thorough insights into imaging data, enabling quantitative research and informed decision-making, as well as facilitating experiment and process optimization, and innovation

In terms of segmentation and classification, we utilize deep learning methodologies such as Segment-Anything, Detectron2, and YOLO to handle complex structures and noisy data.

Light-sheet users can benefit from full brain to atlas registration and segmentation pipelines, enabling cell count at different levels of brain hierarchy.

The fusion of low-resolution CT or MRI images with higher resolution microscopy images can provide both anatomical and functional insights.

The BCF’s image processing and imaging units collaborate to produce high-quality images that meet the necessary signal-to-noise ratio and resolution requirements for effective image processing. This collaborative effort offers the additional benefit of customizing data and image processing solutions using a range of traditional and innovative image-processing tools, including both commercial and open-source analysis software such as Imaris, Image pro premier, FIJI (ImageJ), Matlab, and Python.

High end parallel computing computers and servers are available at the BCF for the benefit of researchers. These run commercial software, and give access to data storage on BCF servers.

Imaging software Publisher Type Description Reservation/ Support
 Imaris Imaris Bitplane Commercial 3D rendering and quantitative segmentation, analysis, tracking, interactions for fluorescence images Computer IMARIS software
 fiji logo ImageJ/FIJI NIH Free Image analysis and processing with extensive plug-ins and macros Contact us
 Zen logo Zen 2.3 Zeiss Commercial (full)


Offline full version for 3D reconstruction, 2D colocalization and LSM880 Airyscan processing Computer IMARIS software
 Zen logo Zen 2.6 Zeiss Commercial (full)


Offline full version for 3D reconstruction, 2D colocalization, LSM880 Airyscan processing and widefield and confocal deconvolution Computer IMARIS software
MRI tool BCF Matlab based custom homemade tool 3D reconstruction and display, volume & intensity measurements, synchronization & comparison, T1, T2, T2* mapping, filtering, co-registration, automatic segmentation Contact us
Custom macros and batch solutions Contact us
 ImageProPremier logo Image Pro Plus

Image Pro Premier 9.3.2

Media Cybernetics Commercial Segmentation, classification, count, measurements for brightfield and 2D fluorescence images Computer analysis 4

Computer Image-pro-prem

  Matlab MathWorks Commercial Numerical computing environment for data analysis and visualization Contact us
Python Python Commercial Scripting and automation language for system integration Contact us
  Adobe Photoshop Adobe Commercial Image, line art and graph juxtaposition for visualization and preparation for publication Contact us
 AutoAligner logo Autoaligner Bitplane Commercial Preprocessing for layer alignment of serial sections in same or different formats Contact us
 Living Image logo Living Image Xenogen/ Perkin Elmer Commercial Offline 2D fluorescence and bioluminescence quantitative data measurements Computer in vivo analysis


New users

Please contact Ariel Shemesh tel. 073-378-1109, to coordinate a meeting.