Image Analysis Computers

We currently have 8 image analysis computers, all of them accessible remotely, whilst 4 are also accessible locally with 4k 48inch displays so you can see your data in its best light. We also have a varied range of commercial software packages available on many of these computers Below is a list of our image analysis machines, please expand to see computer specifications and available software on each computer.

KARR

Huygens 22.10 Professional Zen 3.0 SR ImageJ/FIJI MATLAB 2022a QuPath 0.3.2 Cell Profiler 4.2.1 Ilastik 1.3.3

KARR is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks. As one of our more powerful analysis computers it tends to be used predominantly for working with large datasets (Single files > 200GB), and contains a range of image analysis software designed to utilise the GPU.

CPU	Threadripper PRO 3975WX
RAM	512 GB
GPU	RTX A6000
Storage	8 TB
Access	Remote Only

YONDU

HALO

YONDU is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks. This machine is primarily used for use of one of our HALO license for analysis of histology images using machine learning.

CPU	Threadripper PRO 3975WX
RAM	512 GB
GPU	RTX A6000
Storage	8 TB
Access	Remote Only

Shodan

Arivis 3.6.0 Imaris 9.9.0 Zen 2014 ImageJ/FIJI MATLAB 2022a QuPath 0.3.2 Cell Profiler 4.2.1 Ilastik 1.3.3

Shodan is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks. As one of our more powerful analysis computers it tends to be used predominantly for working with large datasets (Single files > 200GB), and contains a range of software useful in the processing of lightsheet data.

CPU	Threadripper PRO 3975WX
RAM	512 GB
GPU	RTX A5000
Storage	8 TB
Access	Remote Only

Deep Thought

ImageJ/FIJI MATLAB 2022a QuPath 0.3.2 Cell Profiler 4.2.1 Ilastik 1.3.3

Deep Thought is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks. As one of our more powerful analysis computers it tends to be used predominantly for working with large datasets (Single files > 200GB), and contains a range of software useful in the processing of lightsheet data.

CPU	Threadripper PRO 3975WX
RAM	512 GB
GPU	RTX A5000
Storage	8 TB
Access	Remote Only

Orac

Arivis 3.6.0 Imaris 9.9.0 Zen 2014 ImageJ/FIJI MATLAB 2020b QuPath 0.2.3 Cell Profiler 4.0.7 Amira 6.3.0

Orac is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks. As one of our more powerful analysis computers it tends to be used predominantly for working with large datasets (Single files > 200GB), and contains a range of software useful in the processing of lightsheet data.

CPU	2x Intel Xeon e5-2690 v4 @ 2.6 GHz
RAM	256 GB
GPU	NVidea Quadro M6000
Storage	12 TB
Access	Remote Only

Hal

ImageJ/FIJI MATLAB 2020b QuPath 0.2.3 Cell Profiler 4.0.7 Amira 6.3.0

Hal is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks. As one of our more powerful analysis computers it tends to be used predominantly for working with large datasets (Single files > 200GB), and contains a range of software useful in the processing of lightsheet data.

CPU	2x Intel Xeon e5-2690 v4 @ 2.6 GHz
RAM	128 GB
GPU	GeForce GTX 1080
Storage	3 TB
Access	Remote Only

Marvin

Zen Blue 3.0 ImageJ/FIJI MATLAB 2020b QuPath 0.2.3 Cell Profiler 4.0.7 Amira 6.3.0

Marvin is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks. In addition to generic processing tasks using free open source software, Marvin has a license for Zen 3.0. This makes it well suited to processing Airy scan images offline instead of on the microscope.

CPU	2x Intel Xeon e5-2690 v4 @ 2.6 GHz
RAM	128 GB
GPU	GeForce GTX 1080
Storage	3 TB
Access	Remote Only

GLaDOS

ImageJ/FIJI MATLAB 2020b QuPath 0.2.3 Cell Profiler 4.0.7 Amira 6.3.0

Arivis 3.3

GLaDOS is currently the BMIFs fastest computer. A 32 core CPU combined with a 8TB of rapid storage operating on a PCIe v4 motherboard makes this machine ideal for image processing and analysis tasks.

CPU	AMD Ryzen Threadripper 3970X 3.7Ghz
RAM	256 GB
GPU	Nvidea RTX3070 8G
Storage	8 TB
Access	Remote Only

Galatea

ImageJ/FIJI MATLAB 2020b QuPath 0.2.3 Cell Profiler 4.0.7

Galatea is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks.

CPU	AMD Ryzen 9 3900X 3.8GHz
RAM	128 GB
GPU	Nvidia Quadro P4000
Storage	8 TB
Access	Remote Only

VIKI

Imaris 7.2.3 inFOrm 2.4.11 ImageJ/FIJI MATLAB 2019a Zen 3.1 QuPath 0.2.3 Cell Profiler 4.0.7

VIKI is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks.

CPU	2x Intel Xeon Silver 4110 @ 2.1 GHz
RAM	68 GB
GPU	NVIDIA Quadro P2000
Storage	5.5 TB
Access	Remote & Local

Red Queen

Zen 3.1inForm 2.4.11 NIS Elements 5.21.01 ImageJ/FIJI MATLAB 2020b QuPath 0.2.3 Cell Profiler 4.0.7

Red Queen is an image analysis machine that can be accessed remotely for demanding image processing and analysis tasks.

CPU	Intel i7 7820X @ 3.6 GHz
RAM	128 GB
GPU	GeForce RTX 2060
Storage	4 TB
Access	Remote & Local

ED209

ilastik 1.3 SymPhoTime ImageJ/FIJI MATLAB 2020b QuPath 0.2.3 Cell Profiler 4.0.7

ED209 is an image analysis machine that can be accessed remotely or accessed locally in the Biosciences level 2 office area.

CPU	2x Intel Xeon E5 2630 v4 @ 2.2 GHz
RAM	64 GB
GPU	GeForce GTX 1070
Storage	2 TB
Access	Remote & Local

Software Desciptions

Arivis	Arivis Vision4D is a modular software for working with multi-channel 2D, 3D and 4D images of almost unlimited size independent of available RAM. Many imaging systems, such as high speed confocal, Light Sheet/ SPIM and 2 Photon systems, can produce a huge amount of multi-channel data, which arivis Vision4D handles without constraints.
Imaris	Imaris is a popular image analysis software for working with 3D and 4D data sets. It has a collection of tools for segmentation and quantifying 3D metrics, including filament tracing. It also offers attractive 3D rendering functionality for generating stunning movies for presentation.
Zen 2014 SP1	Zen 2014 is a specilised version of Zen, specifically for lighsheet acquisition and analysis. It is used for fusing together datasets acquired on our Zeiss Z.1 lightsheet, including operations such as dual side & multi-view fusion.
Huygens	Huygens can be used for a wide variety of image processing tasks, but its stand out functions are those involving deconvolution. Not only does it have a wide range of algorithms that take into account the type of imaging the dataset was acquired with, but its user interface helps walk you thought the numerous steps which in other software can be more confusing.
ImageJ/FIJI	Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
MATLAB	MATLAB® is a programming platform designed specifically for engineers and scientists. The heart of MATLAB is the MATLAB language, a matrix-based language allowing the most natural expression of computational mathematics. It also comes with a toolset useful for image analysis and processing.
QuPath	QuPath is a new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images
Cell Profiler	CellProfiler is free, open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
Amira	Wherever three-dimensional imaging data sets need to be processed, in life sciences, materials science, natural sciences or industrial inspection applications, Amira-Avizo Software offer abundant state-of-the-art image data processing, exploration and analysis features within an intuitive workflow and easy-to-use graphical user interface.
Stereo Investigator	Stereo Investigator is an unbiased stereology software from MBF Bioscience. Users can setup workflows for the quantitative analysis of cell number, length, area and volumes, as well as subcellular and macrostructures in tissue specimens.
Neurolucida 360	Neurolucida 360 is a 3D neuronal reconstruction software from MBF Biosciences. User can select automatic, semi-automatic and manual tracing to assess different neuronal structures including axons, dendrites and dendritic spines. Neurolucida 360 can be used with single and multichannel datasets and is compatible brightfield and fluorescence images.