Rue du Bugnon 9, CH-1005, Lausanne, VD, Switzerland
+41 21 692 51 06
CIF Coordinator: jean-yves.chatton@unil.ch

Software

This page compiles the list of the image analysis and processing software currently installed and supported in at least one of our antennas.

Bitplane Imaris

Description

Imaris is a commercial 3D Visualization and analysis program. It allows to reconstruct 3D surfaces, detects cells and spot-like objects, trace filaments, and provide statistics and classification.

Imaris showing various types of isosurfaces and Cell objects

Availability

Here are the modules currently available at the CIF :

Last update : 03/06/2021

Module

Total

Staff

Bugnon

Dorigny

Epalinges

Agora

(EMF)

Imaris-Core

6

0

2

1

1

2

1

Imaris-Cell

3

0

1

1

1

1

0

Imaris-Measurement_Pro

6

0

2

1

1

2

1

Imaris-Track

2

0

1

1

0

1

0

Imaris-XT

2

0

1

1

0

1

0

Imaris-Filament_Tracer

2

0

1

0

1

1

0

Imaris-Coloc

4

0

1

1

1

2

0

Possible Workstations

4

CIFA-STA-DES-00
CIFB-STA-DES-00

CIFB-PRO-02
CIFB-PRO-03
CIFB-PRO-04
CIFB-PRO-05

CIFD-PRO-04
CIFD-PRO-05
CIFD-PRO-06

CIFE-PRO-03

CIFA-PRO-01
CIFA-PRO-02

WORKSTATION1110

Imaris-Floating_License_Server

1

 

CIF-LIC-SVR

       

Official website

Link to the product: https://imaris.oxinst.com/


ImageJ / Fiji

Description

Fiji and ImageJ are a free and open-source general purpose bioimage analysis program. It’s the go-to toolbox for any serious microscopist.

Using StarDist with Fiji to detect cell nuclei

Availability

Fiji is installed on every CIF workstation.

Official website

Link to the product: https://fiji.sc/


Nikon NIS-Elements

Description

NIS-Elements is the offline version of the image acquisition software from Nikon, driving every instruments of the same brand.

Considering the size and complexisity of the data coming out the spinning disks, this software is the best suited to deal with Nikon’s native file format, .nd2 files.

Nikon NIS Elements running a cell tracking analysis

Availability

NIS-Elements is installed on every workstation at the Agora, Bugnon, or Dorigny site. We have a pool of 3 floating licenses shared across all these sites.

The optional modules available are :

  • EDF : Extended Depth of Focus, create a focused image from a Z stack.
  • CA FRET : Calcium and FRET dedicated image analysis modules
  • 3D Tracking : Object tracking across time in Z stacks
  • JOBS Viewer : View and edit JOBS automation code
  • General Analysis : Procedural (top to bottom) module for simple analysis routines (threshold, mask, filter, measurements,…)
  • GA3 : General Analysis 3. Node-based analysis builder. Connect and combine processing nodes to build complex analysis workflows.

Official website

Link to the product: https://www.microscope.healthcare.nikon.com/products/software/nis-elements


Zeiss Zen Desk

Description

Zen Desk is the offline version of the Zen Blue image acquisition software from Carl Zeiss, driving every instruments of the same brand.

You can classify regions using a pixel classifier and create charts and customizable result tables.

Zen Desk with specific regions classified based on the pixel values with a fluorescent image.

Availability

The offline Zen desk software is available on the Axioscan Analysis Workstation, next the the Axioscan slide scanner, at the Bugnon campus.

This version has the following modules enabled :

  • Measurement
  • Image Analysis
  • Extended Focus
  • Macro environment
  • Advanced Processing

Official website

Product page: https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html


SVI Huygens Essential Suit

Description

The Huygens Essential suit is composed of several tools revolving around the central theme of image deconvolution.

Huygens Essential interface, with a Twin Slicer window showing the original vs deconvolved image

Availability

Our current licenses include:

  Huygens Essential Huygens Remote Manager
Modality
  • Confocal
  • Spinning Disk
  • Widefield
  • Confocal
  • Spinning Disk
  • Widefield
File formats
  • Additional File Formats
  • Additional File Formats
Computing
  • Server type: small
  • GPU max cores: 24576
  • GPU max memory: 64GB
  • Server type: small
Options
  • Time series
  • PSF Measurement
  • Deconvolution Express
  • Time series

Official website

Link to the product: https://svi.nl/HomePage


QuPath

Description

QuPath, short for Quick Pathology, is a free and open-source software package that allows the visualization and analysis of large images from slide scanners and other similar mosaics.

It handles pyramidal files much better than Fiji, and allows for cell detection and classification using machine learning, with in fluorescence and brightfield modalities.

QuPath showing detected cells in a hand drawn region displayed as a measurement map, as well as detailed features of a single cell and the measurements distribution shown in a graph.

Availability

QuPath is installed on every CIF workstation

Official website

Link to the product: https://qupath.github.io/


CellProfiler

Description

CellProfiler is a free image processing and analysis software package that differs from others by focusing on two main features:

  • Reproducibility by building and sharing processing and analysis pipelines from pre-built modules
  • Automation by including file and data management in its core, making it the default choice for high throughput imaging and its very large amount of files associated with.
CellProfiler showing several output windows after the analysis of an RGB fluorescence image and nuclei detection

Availability

CellProfiler is installed on select CIF workstations. If you need an instance on a workstation where it is not installed, please contact Yannick Krempp.

Official website

Link to the product: https://cellprofiler.org/


Hamamatsu NDP.view 2 and NDP.view2 Plus

Description

NDP.view 2 Plus is the software dedicated to viewing and annotating slides from the Nanozoomeer slide scanner. It can do light image processing (adjustments) and manual analysis like counting cells, draw profiles, create reports …

The free version is limited to .ndpi files and has less features.

The free NDP.view 2 image viewer

Availability

  • The nanozoomer slidescanner at the Epalinges site comes with an offline processing workstation with NDP.view 2 Plus installed.
  • Other workstations in the facility can have NDP.view 2 (free version) installed on request.

Official website

Link to the product page (PDF):