objectCleanse

Removes abnormalities (clipped/debris) from image.

Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.

Yohann Demont

Tools for Imaging Flow Cytometry

Gautier Stoll

Guido Kroemer

Jean-Pierre Marolleau

Loïc Garçon

objectCleanse function

<dl><dt>mat</dt>
<dd>a numeric matrix (image).</dd>
<dt>msk</dt>
<dd>a numeric matrix (mask identifying abnormalities).</dd>
<dt>add_noise</dt>
<dd>if TRUE adds normal noise to background using rnorm(), from Rcpp. Default is TRUE.</dd>
<dt>random_seed</dt>
<dd>a list of elements to pass to <a href="/link/set.seed?package=IFC&version=0.2.1" data-mini-rdoc="IFC::set.seed">set.seed</a> or a single value, interpreted as an integer, or NULL to be used when 'add_noise' is set to TRUE. Default is NULL.
Note that NA_integer_ or list(seed = NA_integer_) can be used to not call <a href="/link/set.seed?package=IFC&version=0.2.1" data-mini-rdoc="IFC::set.seed">set.seed</a> at all.</dd>
<dt>bg</dt>
<dd>mean value of the background added if add_noise is TRUE. Default is 0.</dd>
<dt>sd</dt>
<dd>standard deviation of the background added if add_noise is TRUE. Default is 0.</dd></dl>

Arguments

Object Cleanser — objectCleanse

<dl>

<dt>mat</dt>
<dd>a numeric matrix (image).</dd>


<dt>msk</dt>
<dd>a numeric matrix (mask identifying abnormalities).</dd>


<dt>add_noise</dt>
<dd>if TRUE adds normal noise to background using rnorm(), from Rcpp. Default is TRUE.</dd>


<dt>random_seed</dt>
<dd>a list of elements to pass to <a href='https://rdrr.io/r/base/Random.html'>set.seed</a> or a single value, interpreted as an integer, or NULL to be used when 'add_noise' is set to TRUE. Default is NULL.
Note that NA_integer_ or list(seed = NA_integer_) can be used to not call <a href='https://rdrr.io/r/base/Random.html'>set.seed</a> at all.</dd>


<dt>bg</dt>
<dd>mean value of the background added if add_noise is TRUE. Default is 0.</dd>


<dt>sd</dt>
<dd>standard deviation of the background added if add_noise is TRUE. Default is 0.</dd>

</dl>

objectCleanse: Object Cleanser

Description

Usage

Value

Arguments