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Image analysis and processing software

Just taking an image with a microscope, and keep it in its raw format, might be sufficient for your needs. But often a fluorescent image needs to have a background subtracted and it could get much sharper with deconvolution and a z-stack needs to be put into a 3D image. You might want to quantify intensities or sizes of objects, track structures in a time series or make movies. To do all these things you will need specialized software.

If you need help to create a solution for your specific needs we can assist you. The price for this service depends on the complexity of the problem and will be discussed on a project basis.

Software at CCI

We provide a few commercial image analysis and processing softwares, installed on powerful computers, which are free of charge for our microscopy users:

Volocity - Deconvolution, 3D reconstruction, advanced movie recording, tracking, and quantification. Learn how to use it by watching the instructive on-line tutorials.

scan^R image analysis software - High content screening software from Olympus for analysing large quantities of images, especially those aquired using the scan^R automatic microscope system.

Free software:

There are several free softwares that you can download to your own computer. We also provide these on our image analysis workstations.

Zen lite - With this software you can easily open the images that you have acquired with all our Carl Zeiss microscopes. The software is only compatible with PC.

ImageJ - Developed at NIH, works on both PC and Mac and can open most image file formats. There are also a couple of installation packages, MBF_ImageJ and Fiji, with many plugins already installed.

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

IMOD - is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

eTomo provides a graphical user interface (GUI) to the IMOD Tomography package. aTomo is a program used to reconstruct 3D volumes by joining smaller volumes and/or guiding the user through the process of tomographic reconstruction of single and dual axis tilt series. During this process eTomo make many program calls and often launches 3dmod and Midas to allow users to make fine adjustments.


Older softwares:

LSM Image Browser - With this software you can open the images (database) that you have acquired with our Zeiss LSM 510 Meta system.

AxioVision LE - With this software you can open the images that you have acquired with our Zeiss Axiovert 200 system.

Page Manager: CCI web manager|Last update: 5/11/2016

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