Virus

CXIDB

Submitted by Perrine on Mon, 03/06/2023 - 16:10

The main goal of the Coherent X-ray Imaging Data Bank is to create an open repository for CXI experimental data.

Description

BioImage.IO -- a collaborative effort to bring AI models to the bioimaging community. 

  • Integrated with Fiji, ilastik, ImJoy and more
  • Try model instantly with BioEngine
  • Contribute your models via Github

This is a database of pretrained deep Learning models. 

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Description

Estimate the frequency of hepatitis C virus infected cells based on the intensity of viral antigen associated immunofluorescence. 

The core is an ImageJ Macro, so it's easy to modify for one's own needs (Link to the code). 

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Description

These two similar KNIME workflow solutions take 3D data stacks to segment the spots first, using local thresholding with subsequent morphological operations in order to remove noise. Colocalization is then defined by overlapping or center point distance between segmented objects. Further filtering such as overlapping ratio or distance range is done through KNIME table processing.

Two different types are available. 

  1. colocalization based on overlapping
  2. colocalization based on distance between object centers

Sample images: Smapp_Ori files

Chapter 4 in the documentation.