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quimp-doc's Introduction

About

This is the official documentation for QuimP software.

How to use it

This repository contains LaTeX source of the QuimP documentation. Compiled pdf file related to currently released version of QuimP is available at QuimP homepage. The develop branch follows development version of QuimP, whereas master contains documentation for already released QuimP.

Both branches are compiled to Html/PDF by script that runs daily around 6am and then uploaded to:

  1. http://pilip.lnx.warwick.ac.uk/docs/develop/QuimP_Guide.html - develop branch
  2. http://pilip.lnx.warwick.ac.uk/docs/master/QuimP_Guide.html - master branch

Building

One needs to have full LaTeX distribution installed on the system. Then, to build the documentation type:

cd Docs
pdflatex QuimP_Guide.tex
pdflatex QuimP_Guide.tex
bibtex QuimP_Guide.aux
pdflatex QuimP_Guide.tex
pdflatex QuimP_Guide.tex

The final document is located in Docs/QuimP_Guide.pdf.

Links

quimp-doc's People

Contributors

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Watchers

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Forkers

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quimp-doc's Issues

Update #266

CellDynamics/QuimP#266

Mask image - user can provide binary image, where white areas will stand for the foreground seed. This mode is intended for using results of Active Contour segmentation as input to Random Walk algorithm. The seed stack should have the same size as segmented image. The foreground labels can be larger than objects they label because they are pre-processed (usually shrank) by algorithm selected in Inter-processing section. Typical use case is to perform rough segmentation in BOA module using fail safe parameters which usually lead to rough segmentation and then to use Random Walk plugin to get fine one. The improvements should clearly visible especially in concave areas where Active Contour method fails.

Mention that shrink/expand is usually necessary here.

Include #291

CellDynamics/QuimP#291

Tracking by colors - there can be the same colors if they are separated by at least one frame. Then they will be counted as separate track

ANA options

Mention that image with cortex is an overlay. Say about tables

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