Here you can see the result of those measurements:
- |
let dimension = Filter.squareCalculator 6.45 2. 20. 2.
+let dimension = Filter.squareCalculator 6.45 2. 20. 2.
-let wvRadius = Filter.cellRadiusCalculator 9.5 6.45 2. 20. 2.
+let wvRadius = Filter.cellRadiusCalculator 9.5 6.45 2. 20. 2.
-let processFolders folderPath height width radius multiplier =
- let subfolders = Directory.GetDirectories folderPath
- let result = subfolders
- |> Array.mapi (fun i folder ->
- printfn "processing folder %i of %i" (i+1) subfolders.Length
- Pipeline.processImages folder height width radius multiplier)
- result
+let processFolders folderPath height width radius multiplier =
+ let subfolders = Directory.GetDirectories folderPath
+ let result = subfolders
+ |> Array.mapi (fun i folder ->
+ printfn "processing folder %i of %i" (i+1) subfolders.Length
+ Pipeline.processImages folder height width radius multiplier)
+ result
-let processAll = processFolders @"...\Dilution\CoulterCounter"
- dimension dimension wvRadius 0.2
+let processAll = processFolders @"...\Dilution\CoulterCounter"
+ dimension dimension wvRadius 0.2
The data for the manual counting can be found here, and the Coulter Counter data is here.
A more in depth explanation how to adapt the functions for your use can be found here
-namespace Microsoft.FSharp
-namespace System
-namespace System.IO
-val cellCounter : float []
-val cellCounterStabw : float []
-val manual : float []
-val manualStabw : float []
-val coulterCounter : float []
-val coulterCounterStabw : float []
-val increments : string []
-val xAxis : title:'a -> 'b
-val title : 'a
-val yAxis : title:'a -> 'b
-val chartCellCounter : obj
-val chartManual : obj
-val chartCoulterCounter : obj
-val combinedChart : obj
-val dimension : obj
-val wvRadius : obj
-val processFolders : folderPath:string -> height:'a -> width:'b -> radius:'c -> multiplier:'d -> 'e []
-val folderPath : string
-val height : 'a
-val width : 'b
-val radius : 'c
-val multiplier : 'd
-val subfolders : string []
-type Directory =
static member CreateDirectory : path:string -> DirectoryInfo + 1 overload
static member Delete : path:string -> unit + 1 overload
static member EnumerateDirectories : path:string -> IEnumerable<string> + 2 overloads
static member EnumerateFileSystemEntries : path:string -> IEnumerable<string> + 2 overloads
static member EnumerateFiles : path:string -> IEnumerable<string> + 2 overloads
static member Exists : path:string -> bool
static member GetAccessControl : path:string -> DirectorySecurity + 1 overload
static member GetCreationTime : path:string -> DateTime
static member GetCreationTimeUtc : path:string -> DateTime
static member GetCurrentDirectory : unit -> string
...
-Directory.GetDirectories(path: string) : string []
Directory.GetDirectories(path: string, searchPattern: string) : string []
Directory.GetDirectories(path: string, searchPattern: string, searchOption: SearchOption) : string []
-val result : 'e []
-module Array
from Microsoft.FSharp.Collections
-val mapi : mapping:(int -> 'T -> 'U) -> array:'T [] -> 'U []
-val i : int
-val folder : string
-val printfn : format:Printf.TextWriterFormat<'T> -> 'T
-property System.Array.Length: int
-val processAll : obj []
+Multiple items
namespace FSharp
--------------------
namespace Microsoft.FSharp
+namespace FSharp.Plotly
+namespace CounterFunctions
+namespace System
+namespace System.IO
+val cellCounter : float []
+val cellCounterStabw : float []
+val manual : float []
+val manualStabw : float []
+val coulterCounter : float []
+val coulterCounterStabw : float []
+val increments : string []
+val xAxis : title:'a -> Axis.LinearAxis
+val title : 'a
+module Axis
from FSharp.Plotly
+Multiple items
type LinearAxis =
inherit DynamicObj
new : unit -> LinearAxis
static member init : ?AxisType:AxisType * ?Title:'a * ?Titlefont:Font * ?Autorange:AutoRange * ?Rangemode:RangeMode * ?Range:Range * ?Fixedrange:'b * ?Tickmode:TickMode * ?nTicks:'c * ?Tick0:'d * ?dTick:'e * ?Tickvals:'f * ?Ticktext:'g * ?Ticks:TickOptions * ?Mirror:Mirror * ?Ticklen:'h * ?Tickwidth:'i * ?Tickcolor:'j * ?Showticklabels:'k * ?Tickfont:Font * ?Tickangle:'l * ?Tickprefix:'m * ?Showtickprefix:ShowTickOption * ?Ticksuffix:'q * ?Showticksuffix:ShowTickOption * ?Showexponent:ShowExponent * ?Exponentformat:ExponentFormat * ?Tickformat:'r * ?Hoverformat:'s * ?Showline:'t * ?Linecolor:'a1 * ?Linewidth:'a2 * ?Showgrid:'a3 * ?Gridcolor:'a4 * ?Gridwidth:'a5 * ?Zeroline:'a6 * ?Zerolinecolor:'a7 * ?Zerolinewidth:'a8 * ?Anchor:AxisAnchorId * ?Side:Side * ?Overlaying:AxisAnchorId * ?Domain:Range * ?Position:float * ?IsSubplotObj:'a9 * ?Tickvalssrc:'a10 * ?Ticktextsrc:'a11 * ?Showspikes:'a12 * ?Spikesides:'a13 * ?Spikethickness:'a14 * ?Spikecolor:'a15 * ?Showbackground:'a16 * ?Backgroundcolor:'a17 * ?Showaxeslabels:'a18 -> LinearAxis
static member style : ?AxisType:AxisType * ?Title:'b * ?Titlefont:Font * ?Autorange:AutoRange * ?Rangemode:RangeMode * ?Range:Range * ?Fixedrange:'c * ?Tickmode:TickMode * ?nTicks:'d * ?Tick0:'e * ?dTick:'f * ?Tickvals:'g * ?Ticktext:'h * ?Ticks:TickOptions * ?Mirror:Mirror * ?Ticklen:'i * ?Tickwidth:'j * ?Tickcolor:'k * ?Showticklabels:'l * ?Tickfont:Font * ?Tickangle:'m * ?Tickprefix:'n * ?Showtickprefix:ShowTickOption * ?Ticksuffix:'o * ?Showticksuffix:ShowTickOption * ?Showexponent:ShowExponent * ?Exponentformat:ExponentFormat * ?Tickformat:'p * ?Hoverformat:'q * ?Showline:'r * ?Linecolor:'s * ?Linewidth:'t * ?Showgrid:'a1 * ?Gridcolor:'a2 * ?Gridwidth:'a3 * ?Zeroline:'a4 * ?Zerolinecolor:'a5 * ?Zerolinewidth:'a6 * ?Anchor:AxisAnchorId * ?Side:Side * ?Overlaying:AxisAnchorId * ?Domain:Range * ?Position:float * ?IsSubplotObj:'a7 * ?Tickvalssrc:'a8 * ?Ticktextsrc:'a9 * ?Showspikes:'a10 * ?Spikesides:'a11 * ?Spikethickness:'a12 * ?Spikecolor:'a13 * ?Showbackground:'a14 * ?Backgroundcolor:'a15 * ?Showaxeslabels:'a16 -> (LinearAxis -> LinearAxis)
--------------------
new : unit -> Axis.LinearAxis
+static member Axis.LinearAxis.init : ?AxisType:StyleParam.AxisType * ?Title:'a * ?Titlefont:Font * ?Autorange:StyleParam.AutoRange * ?Rangemode:StyleParam.RangeMode * ?Range:StyleParam.Range * ?Fixedrange:'b * ?Tickmode:StyleParam.TickMode * ?nTicks:'c * ?Tick0:'d * ?dTick:'e * ?Tickvals:'f * ?Ticktext:'g * ?Ticks:StyleParam.TickOptions * ?Mirror:StyleParam.Mirror * ?Ticklen:'h * ?Tickwidth:'i * ?Tickcolor:'j * ?Showticklabels:'k * ?Tickfont:Font * ?Tickangle:'l * ?Tickprefix:'m * ?Showtickprefix:StyleParam.ShowTickOption * ?Ticksuffix:'q * ?Showticksuffix:StyleParam.ShowTickOption * ?Showexponent:StyleParam.ShowExponent * ?Exponentformat:StyleParam.ExponentFormat * ?Tickformat:'r * ?Hoverformat:'s * ?Showline:'t * ?Linecolor:'a1 * ?Linewidth:'a2 * ?Showgrid:'a3 * ?Gridcolor:'a4 * ?Gridwidth:'a5 * ?Zeroline:'a6 * ?Zerolinecolor:'a7 * ?Zerolinewidth:'a8 * ?Anchor:StyleParam.AxisAnchorId * ?Side:StyleParam.Side * ?Overlaying:StyleParam.AxisAnchorId * ?Domain:StyleParam.Range * ?Position:float * ?IsSubplotObj:'a9 * ?Tickvalssrc:'a10 * ?Ticktextsrc:'a11 * ?Showspikes:'a12 * ?Spikesides:'a13 * ?Spikethickness:'a14 * ?Spikecolor:'a15 * ?Showbackground:'a16 * ?Backgroundcolor:'a17 * ?Showaxeslabels:'a18 -> Axis.LinearAxis
+module StyleParam
from FSharp.Plotly
+type Mirror =
| True
| Ticks
| False
| All
| AllTicks
static member convert : (Mirror -> obj)
static member toString : (Mirror -> string)
+union case StyleParam.Mirror.All: StyleParam.Mirror
+type TickMode =
| Auto
| Linear
| Array
static member convert : (TickMode -> obj)
static member toString : (TickMode -> string)
+union case StyleParam.TickMode.Auto: StyleParam.TickMode
+type TickOptions =
| Outside
| Inside
| Empty
static member convert : (TickOptions -> obj)
static member toString : (TickOptions -> string)
+union case StyleParam.TickOptions.Inside: StyleParam.TickOptions
+Multiple items
type Font =
inherit DynamicObj
new : unit -> Font
static member init : ?Family:FontFamily * ?Size:'b * ?Color:'c * ?Familysrc:'d * ?Sizesrc:'e * ?Colorsrc:'f -> Font
static member style : ?Family:FontFamily * ?Size:'a0 * ?Color:'a1 * ?Familysrc:'a2 * ?Sizesrc:'a3 * ?Colorsrc:'a4 -> (Font -> Font)
--------------------
new : unit -> Font
+static member Font.init : ?Family:StyleParam.FontFamily * ?Size:'b * ?Color:'c * ?Familysrc:'d * ?Sizesrc:'e * ?Colorsrc:'f -> Font
+type FontFamily =
| Arial
| Balto
| Courier_New
| Droid_Sans
| Droid_Serif
| Droid_Sans_Mono
| Gravitas_One
| Old_Standard_TT
| Open_Sans
| Overpass
...
static member convert : (FontFamily -> obj)
static member toString : (FontFamily -> string)
+union case StyleParam.FontFamily.Arial: StyleParam.FontFamily
+val yAxis : title:'a -> Axis.LinearAxis
+val chartCellCounter : GenericChart.GenericChart
+type Chart =
static member Area : xy:seq<#IConvertible * #IConvertible> * ?Name:string * ?ShowMarkers:bool * ?Showlegend:bool * ?MarkerSymbol:Symbol * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Dash:DrawingStyle * ?Width:'a4 -> GenericChart
static member Area : x:seq<#IConvertible> * y:seq<#IConvertible> * ?Name:string * ?ShowMarkers:bool * ?Showlegend:bool * ?MarkerSymbol:Symbol * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Dash:DrawingStyle * ?Width:'a4 -> GenericChart
static member Bar : keysvalues:seq<#IConvertible * #IConvertible> * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Marker:Marker -> GenericChart
static member Bar : keys:seq<#IConvertible> * values:seq<#IConvertible> * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Marker:Marker -> GenericChart
static member BoxPlot : xy:seq<'a0 * 'a1> * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Fillcolor:'a3 * ?Opacity:float * ?Whiskerwidth:'a4 * ?Boxpoints:Boxpoints * ?Boxmean:BoxMean * ?Jitter:'a5 * ?Pointpos:'a6 * ?Orientation:Orientation -> GenericChart
static member BoxPlot : ?x:'a0 * ?y:'a1 * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Fillcolor:'a3 * ?Opacity:float * ?Whiskerwidth:'a4 * ?Boxpoints:Boxpoints * ?Boxmean:BoxMean * ?Jitter:'a5 * ?Pointpos:'a6 * ?Orientation:Orientation -> GenericChart
static member Bubble : xysizes:seq<#IConvertible * #IConvertible * #IConvertible> * ?Name:string * ?Showlegend:bool * ?MarkerSymbol:Symbol * ?Color:'a3 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font -> GenericChart
static member Bubble : x:seq<#IConvertible> * y:seq<#IConvertible> * sizes:seq<#IConvertible> * ?Name:string * ?Showlegend:bool * ?MarkerSymbol:Symbol * ?Color:'a3 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font -> GenericChart
static member ChoroplethMap : locations:seq<string> * z:seq<#IConvertible> * ?Text:seq<#IConvertible> * ?Locationmode:LocationFormat * ?Autocolorscale:bool * ?Colorscale:Colorscale * ?Colorbar:'a2 * ?Marker:Marker * ?Zmin:'a3 * ?Zmax:'a4 -> GenericChart
static member Column : keysvalues:seq<#IConvertible * #IConvertible> * ?Name:string * ?Showlegend:bool * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#IConvertible> * ?TextPosition:TextPosition * ?TextFont:Font * ?Marker:Marker -> GenericChart
...
+static member Chart.Line : xy:seq<#System.IConvertible * #System.IConvertible> * ?Name:string * ?ShowMarkers:bool * ?Showlegend:bool * ?MarkerSymbol:StyleParam.Symbol * ?Color:'a2 * ?Opacity:float * ?Labels:seq<#System.IConvertible> * ?TextPosition:StyleParam.TextPosition * ?TextFont:Font * ?Dash:'a4 * ?Width:'a5 -> GenericChart.GenericChart
static member Chart.Line : x:seq<#System.IConvertible> * y:seq<#System.IConvertible> * ?Name:string * ?ShowMarkers:bool * ?Showlegend:bool * ?MarkerSymbol:StyleParam.Symbol * ?Color:'c * ?Opacity:float * ?Labels:seq<#System.IConvertible> * ?TextPosition:StyleParam.TextPosition * ?TextFont:Font * ?Dash:'e * ?Width:'f -> GenericChart.GenericChart
+static member Chart.withYErrorStyle : ?Array:'a * ?Arrayminus:'b * ?Symmetric:'c * ?Color:'d * ?Thickness:'e * ?Width:'f -> (GenericChart.GenericChart -> GenericChart.GenericChart)
+static member Chart.withTraceName : ?Name:string * ?Showlegend:bool * ?Legendgroup:string * ?Visible:StyleParam.Visible -> (GenericChart.GenericChart -> GenericChart.GenericChart)
+val chartManual : GenericChart.GenericChart
+val chartCoulterCounter : GenericChart.GenericChart
+val combinedChart : GenericChart.GenericChart
+static member Chart.Combine : gCharts:seq<GenericChart.GenericChart> -> GenericChart.GenericChart
+static member Chart.withX_Axis : xAxis:Axis.LinearAxis * ?Id:int -> (GenericChart.GenericChart -> GenericChart.GenericChart)
+static member Chart.withY_Axis : yAxis:Axis.LinearAxis * ?Id:int -> (GenericChart.GenericChart -> GenericChart.GenericChart)
+static member Chart.withSize : width:float * heigth:float -> (GenericChart.GenericChart -> GenericChart.GenericChart)
+val dimension : int
+module Filter
from CounterFunctions
+val squareCalculator : cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> int
+val wvRadius : float
+val cellRadiusCalculator : cellDiameter:float -> cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> float
+val processFolders : folderPath:string -> height:int -> width:int -> radius:float -> multiplier:float -> (int * GenericChart.GenericChart) [] []
+val folderPath : string
+val height : int
+val width : int
+val radius : float
+val multiplier : float
+val subfolders : string []
+type Directory =
static member CreateDirectory : path:string -> DirectoryInfo
static member Delete : path:string -> unit + 1 overload
static member EnumerateDirectories : path:string -> IEnumerable<string> + 2 overloads
static member EnumerateFileSystemEntries : path:string -> IEnumerable<string> + 2 overloads
static member EnumerateFiles : path:string -> IEnumerable<string> + 2 overloads
static member Exists : path:string -> bool
static member GetCreationTime : path:string -> DateTime
static member GetCreationTimeUtc : path:string -> DateTime
static member GetCurrentDirectory : unit -> string
static member GetDirectories : path:string -> string[] + 2 overloads
...
+Multiple items
Directory.GetDirectories(path: string) : string []
Directory.GetDirectories(path: string, searchPattern: string) : string []
Directory.GetDirectories(path: string, searchPattern: string, searchOption: SearchOption) : string []
--------------------
Directory.GetDirectories(path: string) : string []
Directory.GetDirectories(path: string, searchPattern: string) : string []
Directory.GetDirectories(path: string, searchPattern: string, searchOption: SearchOption) : string []
+val result : (int * GenericChart.GenericChart) [] []
+module Array
from Microsoft.FSharp.Collections
+val mapi : mapping:(int -> 'T -> 'U) -> array:'T [] -> 'U []
+val i : int
+val folder : string
+val printfn : format:Printf.TextWriterFormat<'T> -> 'T
+property System.Array.Length: int
+module Pipeline
from CounterFunctions
+val processImages : folderPath:string -> height:int -> width:int -> radius:float -> multiplier:float -> (int * GenericChart.GenericChart) []
+val processAll : (int * GenericChart.GenericChart) [] []
diff --git a/FunctionExplanation.html b/FunctionExplanation.html
index 35fb308..c51da8e 100644
--- a/FunctionExplanation.html
+++ b/FunctionExplanation.html
@@ -40,7 +40,7 @@ 1:
Filter.squareCalculator cameraPixelSize binning magnification cameraMount
+Filter.squareCalculator cameraPixelSize binning magnification cameraMount
1:
Filter.cellRadiusCalculator cellDiameter cameraPixelSize binning magnification cameraMount
+Filter.cellRadiusCalculator cellDiameter cameraPixelSize binning magnification cameraMount
Process
a square from the counting chamber. It also serves rather as an example of how to use the functions, since it can be modified in several ways, which are detailed below.
1:
Pipeline.processImage filePath height width radius thresholdMultiplier
+Pipeline.processImage filePath height width radius thresholdMultiplier
@@ -74,7 +74,7 @@ Process
you have to open FSharp.Plotly and use the command Chart.Show.
1:
Pipeline.processImages folderPath height width radius thresholdMultiplier
+Pipeline.processImages folderPath height width radius thresholdMultiplier
@@ -86,7 +86,7 @@ Possibl
To count cells in petri dishes, the Filter.rectangleSelectorCenter function in the pipeline has to be replaced with:
1:
Filter.circleSelector pointAXY pointBXY
+Filter.circleSelector pointAXY pointBXY
@@ -95,7 +95,7 @@ Possibl
of the picture, following function can be used:
1:
Filter.rectangleSelector upperLeftXY lowerRightBXY
+Filter.rectangleSelector upperLeftXY lowerRightBXY
@@ -104,7 +104,17 @@ Misc
The functions in the modules Maxima and Image are adapted from the BioFSharp library, an open source bioinformatics toolbox written in F#.
The functions were modified to fit the needs of the Cell Counter.
-namespace Microsoft.FSharp
+Multiple items
namespace FSharp
--------------------
namespace Microsoft.FSharp
+namespace FSharp.Plotly
+namespace CounterFunctions
+module Filter
from CounterFunctions
+val squareCalculator : cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> int
+val cellRadiusCalculator : cellDiameter:float -> cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> float
+module Pipeline
from CounterFunctions
+val processImage : filePath:string -> height:int -> width:int -> radius:float -> multiplier:float -> int * GenericChart.GenericChart
+val processImages : folderPath:string -> height:int -> width:int -> radius:float -> multiplier:float -> (int * GenericChart.GenericChart) []
+val circleSelector : image:float [,] -> float * float -> float * float -> float [] []
+val rectangleSelector : image:float [,] -> int * int -> int * int -> float [] []
diff --git a/index.html b/index.html
index a1488bf..f7d98ce 100644
--- a/index.html
+++ b/index.html
@@ -60,13 +60,13 @@ Example
6:
7:
open CounterFunctions
-open FSharp.Plotly
+open CounterFunctions
+open FSharp.Plotly
-let dimension = Filter.squareCalculator 6.45 2. 20. 2.
+let dimension = Filter.squareCalculator 6.45 2. 20. 2.
-let processedImage = Pipeline.processImage @"...\CellCounter\docsrc\files\img\4.tif"
- dimension dimension 20. 0.2
+let processedImage = Pipeline.processImage @"...\CellCounter\docsrc\files\img\4.tif"
+ dimension dimension 20. 0.2
License file in the GitHub repository.
-namespace Microsoft.FSharp
-val dimension : obj
-val processedImage : obj
+namespace CounterFunctions
+Multiple items
namespace FSharp
--------------------
namespace Microsoft.FSharp
+namespace FSharp.Plotly
+val dimension : int
+module Filter
from CounterFunctions
+val squareCalculator : cameraPixelSize:float -> binning:float -> magnification:float -> cameraMount:float -> int
+val processedImage : int * GenericChart.GenericChart
+module Pipeline
from CounterFunctions
+val processImage : filePath:string -> height:int -> width:int -> radius:float -> multiplier:float -> int * GenericChart.GenericChart