Software for imaging and microscopy
Free tools for HREM image stacks, 3D visualisation and spectral analysis, plus custom software development for optical systems and microscopy hardware.
ABOUT OUR SOFTWARE
Microscopy and imaging software
developed in-house
Indigo Scientific develops specialist software for microscopy, imaging and spectroscopy. Tools built specifically to work with the equipment we supply and the data formats our customers use every day. All of our own software tools are free to download for any user, with no licence fees or subscriptions.
Our free tools cover the full HREM workflow from viewing and navigating large TIF/TIFF image stacks, editing and processing 2D image sequences, montaging and stitching, 3D volumetric visualisation and spectral analysis of forensic fibre data. Each tool is designed to run without requiring high-specification hardware.
Beyond our own tools, we also supply and support manufacturer software from Jenoptik, Tucsen and Zeiss for the cameras and microscopes we distribute in the UK. And for customers with specific requirements, our team offers custom software development for optical systems, spectrometers and hardware control.
Free imaging tools
Tools for HREM image stacks, 3D viewing, image stitching and spectral analysis — all free to download.
Custom software development
Software for optical systems, spectrometers, hardware control and image processing pipelines.
Software by application
Find the right software for your specific imaging application including HREM, fluorescence, live cell and more.
Manufacturer software
Download links and support for Jenoptik Gryphax, Tucsen Mosaic and Zeiss ZEN camera software.
Free to download
Indigo Scientific imaging tools
All five tools below are free for any user — no licence, no subscription. Designed specifically for HREM image data and microscopy workflows.
Software
Image stitching and montaging tool for microscopy datasets. Manually or automatically montage image series, align image stacks on the Z axis and interpolate stacks. Designed specifically for HREM systems and large tile scans.
Software
Image stitching and montaging tool for microscopy datasets. Manually or automatically montage image series, align image stacks on the Z axis and interpolate stacks. Designed specifically for HREM systems and large tile scans.
Software
Visualise 3D datasets without complex processing pipelines. Select an image stack and view immediately in 3D. Slice manually, adjust window and level, control opacity and colour type.
Software
View ONYX spectral data as interactive plots. Zoom, pan and click to extract data points from spectral curves. Save outputs as images. A lightweight viewer for spectral analysis without manipulating raw data files.
Software
A simple pan and zoom viewer built for high-resolution TIF/TIFF image stacks and multipage files. Resizes images on input to reduce lag. Built to handle the large files HREM produces without requiring a powerful workstation.
CAMERA SOFTWARE
Manufacturer software for microscope cameras
Download and support links for the camera control and acquisition software supplied with the microscope cameras we distribute in the UK. All are free to download with your camera purchase.
Software
Control and capture software for Jenoptik GRYPHAX cameras. Acquisition, processing and export tools for the full Jenoptik camera range including Rigel and Arktur.
Software
ZEN is the acquisition and analysis platform for Zeiss microscopes and cameras. Control, capture and process images from Zeiss Axiovert, Axiocam and other Zeiss systems.
Optical system control
Hardware control software for custom optical instruments, filter wheels, stages and illumination systems.
Spectrometer software
Acquisition, display and analysis software for spectrometer and spectral imaging systems.
Image proecessing software
Batch processing, format conversion and automated analysis workflows for large microscopy datasets.
Data export & reporting
Custom export formats, reporting tools and database integration for research and quality management.
CUSTOM DEVELOPMENT
Software built around your system
Standard software doesn't always fit. If you have a specific instrument, unusual data format or a workflow that needs automating, our team can design and develop software around it.
We have experience building control software for optical systems, spectrometers and custom imaging hardware, as well as image processing pipelines and data export tools for research and industrial customers.
Translation tools stitched image of mouse HREM sample
Translation Tool for Microscopy Images
Translation Tools is a simple yet effective image stitching tool for performing different operations that require X/Y/Z shift and more. Primarily used for our Optical HREM systems for creating high resolution montages without a powerful PC or complex feature finding (when there may not be any features).
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Manually Montage Microscope Images (for a series or just one)
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Automatically Montage Microscope Images (for a series or just one)
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Align Image Stacks on the Z Axis
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Interpolate and Image Stack
This software package can be downloaded for free for all
3D Viewer for Volumetric Datasets
Visualise 3D datasets without complex processing, combine pipelines with 3D viewing. Simply select the image stack and click process to view the images in 3D.
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Visualise 3D datasets while sectioning
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View whole structures at varying resolutions based on PC specifications
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Slice view manually to view internal structures
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Adjust window/level, colour type, opacity and more
This software package can be downloaded for free for all
3D Sample of HREM
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Tif Stack Viewer with Mouse HREM Sample
Image Viewer for Serial Datasets
Flick through whole directories of images with just one click with the serial image viewer for TIF and TIFF files.
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Use a trackbar to index images directly without repetitive clicking
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A simple to use pan and zoom image viewer for high resolution image analysis
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Resize high resolution images on input to reduce lag of viewing
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View TIF/TIFF stacks and multipage files
This software package can be downloaded for free for all
2D Stack Editor for Serial Datasets
Edit whole image stacks with a simple processing tool, with reversible steps and block style addons.
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Process multiple stacks into one
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Calibrate images as Tif and Tiff
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View histograms and images at any point in the workflow
This software package can be downloaded for free for all
Edited HREM Stack Image with Histogram Output
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ONYX Spectral Viewer with Filter Analysis
Spectral Viewer for ONYX Files
View spectral plots in a graph format with the Spectral Viewer. The lightweight package comes equipped to visualise without manipulating the data.
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Interact with the plot with zooming and panning
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Click to get data points
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Save as an image
This software package can be downloaded for free for all