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Welcome to the FARSIGHT Project Wiki. This Project is Developing Quantitative Tools for Studying Complex and Dynamic Biological Microenvironments from 4D/5D Microscopy Data. Powered by this new Golden Age of optical microscopy:. Modern optical microscopes can capture multi-dimensional images of tissue microenvironments. First of all, these microscopes can record three-dimensional ( x. In addition to traditional morphological measurements (we call them intrinsic measurements. One application of FARSIGHT i...

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Welcome to the FARSIGHT Project Wiki. This Project is Developing Quantitative Tools for Studying Complex and Dynamic Biological Microenvironments from 4D/5D Microscopy Data. Powered by this new Golden Age of optical microscopy:. Modern optical microscopes can capture multi-dimensional images of tissue microenvironments. First of all, these microscopes can record three-dimensional ( x. In addition to traditional morphological measurements (we call them intrinsic measurements. One application of FARSIGHT i...

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1 main page

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9 recently added pages

10 nucleus editor

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FarsightWiki | farsight-toolkit.org Reviews

https://farsight-toolkit.org

Welcome to the FARSIGHT Project Wiki. This Project is Developing Quantitative Tools for Studying Complex and Dynamic Biological Microenvironments from 4D/5D Microscopy Data. Powered by this new Golden Age of optical microscopy:. Modern optical microscopes can capture multi-dimensional images of tissue microenvironments. First of all, these microscopes can record three-dimensional ( x. In addition to traditional morphological measurements (we call them intrinsic measurements. One application of FARSIGHT i...

INTERNAL PAGES

farsight-toolkit.org

1

Seed Editor - FarsightWiki

http://www.farsight-toolkit.org/wiki/Seed_Editor

Open Image and Seed (Location) File. 2 The second view (bottom left) is the YZ or the Sagittal view at the location of the handle. This view is updated whenever the handle in the Volume view or Axial view moves to a new point. 3 The third view (bottom right) is the XY or the Axial view at the location of the handle.This view is updated whenever the handle in the Volume view or Sagittal view moves to a new point. Click on the image to enlarge. Open Image and Seed (Location) File. After the [APPLY] button ...

2

SuperEllipseTrace3D - FarsightWiki

http://www.farsight-toolkit.org/wiki/SuperEllipseTrace3D

Local vascular modelling using Superellipsoid. Vascular local shape modelling using superellipsoid. Robust Vascular Intensity model. Generalized likelihood ratio test. Traversing Vessels Using Superellipsoid. Local vascular modelling using Superellipsoid. Vascular local shape modelling using superellipsoid. Shows the boundary of a superellispoid while the shape parameter ε. Is varied between 1.0 and 0.25 and ε. Is set to 1. The line labelled σ. Where the parameters ε = (ε. The 2-D level curves are ellipt...

3

Segmentation Viewer - FarsightWiki

http://www.farsight-toolkit.org/wiki/Segmentation_Viewer

A Segmentation Viewer is available inside of the Nuclear Segmentation module. The purpose of this viewer is to display segmentation output using graph coloring, so that neighboring segmented objects are colored differently and thus distinguishable from each other. This proves useful in visualizing segmentation results for user validation. Example of Segmentation Viewer Rendering. Example of Rendered Segmentation Error in Lower Right Corner (Green). 10 10 2.0 mySegmentationOutput.tiff. Test data (seen in ...

4

MDL Neuron Modeling - FarsightWiki

http://www.farsight-toolkit.org/wiki/MDL_Neuron_Modeling

The Minimum Description Length (MDL) principle was developed by Rissanen in 1978 and it has its root in information theory [1]. It was generated from Shannon’s classic statistical communication theory [2] and Solomonoff’s inductive inference theory [3]. The original idea is to minimize the codes in terms of binary digits (bits) of a signal to be sent over a communication channel and be decoded on the other side of the channel. Grayscale Skeletonization of Dendrites and Spines. Anisotropic diffusion can s...

5

Validation Methods - FarsightWiki

http://www.farsight-toolkit.org/wiki/Validation_Methods

Validation, Performance Assessment, and Quality Control. Data from Physical Phantoms. Limitations of the Multi-observer Gold Standard. Making it Even Faster: Cluster Editing. Making it Smarter: Pattern Analysis. Putting these Ideas Together: PACE. Workflows for Validation, Performance Assessment, and Quality Control. Validation, Performance Assessment, and Quality Control. It means that the results meet certain performance criteria. Such as sufficiently low bias, and variance (more below). This is the pr...

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nic.ucsf.edu

start [NIC Wiki]

http://nic.ucsf.edu/dokuwiki

Nikon Imaging Center at UCSF / QB3 Wiki. This wiki will be used for general information about microscopy and microscopy-related science and technology that may be of interest to both the UCSF community and the broader microscopy community. If you would like to contribute to the wiki, please email kurt.thorn@ucsf.edu to get an account (we have disabled signups due to spam). Nikon Imaging Center Microscopes. Other equipment and objectives. Deconvolution Workstation 1 (older). Accessing the NIC Server.

stim.ee.uh.edu

NetMets - STIM Laboratory

http://stim.ee.uh.edu/resources/software/netmets

Scalable Tissue Imaging and Modeling. ECE 3340 - Numerical Methods. ECE 6397 - GPU Programming. External Resources: Tutorials, Books, Guides. NetMets provides a metric for comparing the spatial geometry and connectivity of two interconnected graphs, like those produced using neuron and vascular/microvascular centerline segmentation. Networks can be provided in either SWC or OBJ format and can have interconnected components (such as cycles). Value describing the metric tolerance:. GFPR gFNR cFPR cFNR.

openmicroscopy.org

The OME Teams — OME

http://www.openmicroscopy.org/site/about/who-ome

OME Model and Formats. Job Openings with OME. OME - Open Microscopy Environment. The Open Microscopy Environment (OME) is a multi-site collaborative effort among academic laboratories and a number of commercial entities, that produces open tools to support data management for biological light microscopy. Designed to interact with existing commercial software, all OME formats and software are free, and all OME source code is available under the GNU General public license. Map of OME sites. Extend the func...

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Farsight Systems - Travel far and wide

December 9, 2015. Reunion Time In France. Many people from many different backgrounds and of many different ages and group dynamics choose to go caravanning in France every year, but such holidays are perhaps most popular with families with young children. Then you arrive and realise that actually a journey of twice that duration and length would be worth it for the experience of relaxing at a well-serviced caravan park by the beach. This is part of the country that’s still very popular amongst French fo...

farsight-toolkit.org

FarsightWiki

Welcome to the FARSIGHT Project Wiki. This Project is Developing Quantitative Tools for Studying Complex and Dynamic Biological Microenvironments from 4D/5D Microscopy Data. Powered by this new Golden Age of optical microscopy:. Modern optical microscopes can capture multi-dimensional images of tissue microenvironments. First of all, these microscopes can record three-dimensional ( x. In addition to traditional morphological measurements (we call them intrinsic measurements. One application of FARSIGHT i...

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