Supported Software - FrancisCrickInstitute/Image-Analysis-Group GitHub Wiki

Supported Software

We support a variety of image analysis software. We try to stick to open source solutions as often as we can, and we encourage our users to do the same. Please click on a software to get a more detailed description

Open Source Software:

  • FIJI -- General Image Analysis Tool and Viewer. This is generally the first thing we recommend trying.
  • CellProfiler -- Powerful pipeline analysis tool, great for making measurements of segmentable objects
  • Ilastik -- 2D/3D pixel based machine learning classifier. Quickly train a model to differentiate between object/texture classes on a set of images
  • StarDist -- 2D/3D object based segmentation. Particularly useful for nuclei and other roundish objects
  • CellPose -- 2D/3D object based segmentation. Particularly useful for cells and other oddly shaped objects
  • QuPath -- 2D segmentation for whole slide.
  • OMERO -- image database system

Commercial Software

  • Imaris -- 3D Image Viewer, capable of 3D image analysis and pixel based classifier similar to Ilastik. Floating licenses available to Crick Employees
  • MATLAB -- Programming software suite with Image Analysis capabilities. License available for all Crick Employees.

Supported Languages

  • Python -- Dave, Todd, Vanessa
  • Java -- Dave
  • Matlab -- Dave, Todd
  • Fiji Scripting Language -- Dave, Todd, ChatGPT
  • C - Greg Mashanov
  • Fortran - Greg Mashanov

Software installation

FIJI

Download FIJI Here
FIJI is a general purpose image analysis and scripting tool, that comes complete with many useful 'plugins'. In FIJI, a 'plugin' is simply an extension that adds functionality.

FIJI can locally be installed on your computer simply by downloading and unzipping the file from here.

  1. Download FIJI
  2. Move zip file to a folder where you want to install FIJI
  3. Unzip FIJI
  4. Look in the folder you unzipped FIJI in, there should be a folder called Fiji.App
  5. In Fiji.App there should be a program file ImageJ_*** that you double click to run FIJI

FIJI On The Cluster

FIJI can be run on the cluster. We recommend using FIJI on the OnDemand Desktop, and not using the FIJI app supplied by HPC. To download FIJI for use on HPC, follow these directions

CellProfiler

You can download CellProfiler here. There is extensive documentation on the CellProfiler website about how to use it. CellProfiler GUI is the best way to generate a pipeline to do your image analysis. We run frequent CellProfiler classes on how to create a pipeline. For prototyping a pipeline it is generally sufficient to use a standard computer. For medium to large scale image sets, we have CellProfiler installed on a few Image analysis Workstations. Our VM_IM system is able to read/write directly to NEMO storage fairly quickly, and is a good computer for medium to large scale image sets.

CellProfiler on HPC

For installing and running CellProfiler as an individual instance in your working directory on HPC/Nemo, please read the documentation here.

We currently do support CellProfiler on the HPC cluster for running pipelines headless. This is a good idea if you have a very large image set. For help running CellProfiler on the cluster, please contact Todd.

Ilastik

You can download Ilastik here. Ilastik is a pixel based classifier, that works in both 2D and 3D. It is very powerful at segmentation by color, intensity, texture and other pixel based parameters. To use it, you "simply" paint with your mouse cursor the background of your image, as well as representative regions that you are trying to segment. This is done iteratively to create a good pixel classifier that can be run on many images, either through Ilastik or imported into your FIJI or CellProfiler pipelines. We support Ilastik on some of our Image Analysis Workstations and on the Nemo Compute Cluster (HPC).

For directions on how to use Ilastik on the HPC cluster, please read here

QuPath

You can download QuPath here.

Installing QuPath on your Personal Computer

You will need to download and unzip the file on your computer. Please follow the directions for Mac and Windows here

Installing QuPath on nemo

  • Open up an OnDemand GPU Desktop. For instructions on how to do this, see this documentation.
  • Follow the instructions here.

StarDist

StarDist is a python library and machine learning model used primarily to identify nuclei.

CellPose

Omero