ExtractImages_toMatrix

Function to shortcut extraction, normalization and eventually colorization of images to matrix ! excludes mask.

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

ExtractImages_toMatrix function

<dl><dt>...</dt>
<dd>arguments to be passed to <code>objectExtract</code> with the exception of <code>'ifd'</code> and <code>'bypass'</code>(=TRUE). 
/!\ If not any of <code>'fileName'</code>, <code>'info'</code> and <code>'param'</code> can be found in <code>'...'</code> then <code>attr(offsets, "fileName_image")</code> will be used as <code>'fileName'</code> input parameter to pass to <code>objectParam</code>.</dd>
<dt>objects</dt>
<dd>integer vector, IDEAS objects ids numbers to use.
This argument is not mandatory, if missing, the default, all objects will be used.</dd>
<dt>offsets</dt>
<dd>object of class `IFC_offset`.
This argument is not mandatory but it may allow to save time for repeated image export on same file. 
If <code>'offsets'</code> are not provided, extra arguments can also be passed with <code>'...'</code> to <code>getOffsets</code>.</dd>
<dt>display_progress</dt>
<dd>whether to display a progress bar. Default is TRUE.</dd></dl>

Arguments

Shortcut for Batch Images Extraction to Matrices/Arrays — ExtractImages_toMatrix

<dl>

<dt>...</dt>
<dd>arguments to be passed to <code>objectExtract</code> with the exception of <code>'ifd'</code> and <code>'bypass'</code>(=TRUE). 
/!\ If not any of <code>'fileName'</code>, <code>'info'</code> and <code>'param'</code> can be found in <code>'...'</code> then <code>attr(offsets, "fileName_image")</code> will be used as <code>'fileName'</code> input parameter to pass to <code>objectParam</code>.</dd>


<dt>objects</dt>
<dd>integer vector, IDEAS objects ids numbers to use.
This argument is not mandatory, if missing, the default, all objects will be used.</dd>


<dt>offsets</dt>
<dd>object of class `IFC_offset`.
This argument is not mandatory but it may allow to save time for repeated image export on same file. 
If <code>'offsets'</code> are not provided, extra arguments can also be passed with <code>'...'</code> to <code>getOffsets</code>.</dd>


<dt>display_progress</dt>
<dd>whether to display a progress bar. Default is TRUE.</dd>

</dl>

ExtractImages_toMatrix: Shortcut for Batch Images Extraction to Matrices/Arrays

Description

Usage

Value

Arguments

Details