diff --git a/DESCRIPTION b/DESCRIPTION
index 3570321..5c99ce3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: LEEF.2.measurement.flowcytometer
 Type: Package
 Title: What the Package Does (Title Case)
-Version: 0.9.5
+Version: 0.9.7
 Authors@R: c(
   person(given = "Rainer M.", family = "Krug", email = "Rainer.Krug@uzh.ch", role = c("aut", "cre")),
   person("SNF Project 310030_188431", role = "fnd")
diff --git a/NAMESPACE b/NAMESPACE
index 980a123..56ee714 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,11 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
 export(add_new_data)
+export(calculate_gates)
+export(calculate_gates_H)
+export(dens)
+export(dens_H)
+export(extract_traits)
 export(extractor_flowcytometer)
-export(extractor_flowcytometer_gating)
+export(extractor_flowcytometer_density)
 export(extractor_flowcytometer_preparation)
 export(extractor_flowcytometer_traits)
-export(gating)
+export(extractor_traits)
 export(load_parameter)
 export(par_template)
 export(pre_processor_flowcytometer)
diff --git a/R/dens.R b/R/dens.R
index dee1c05..0f377db 100644
--- a/R/dens.R
+++ b/R/dens.R
@@ -26,7 +26,7 @@ dens <- function(
   # #----- HAVING A LOOK AT THE GATING -----#
 
   # i <- 1
-  # flowViz::xyplot(`FL3-A` ~ `FL1-A`, data = fsa[[i]], filter = bacteria_gate)
+  # flowViz::xyplot(`FL3-A` ~ `FL1-A`, data = fsa[[i]], filter = gates$bacteria$bacteria_gate)
   # # fsa[[i]]
   # flowViz::densityplot(~ `FL1-A`, data = fsa[[i]], filter = rg_LNA)
   # # fsa[[i]]
@@ -42,7 +42,7 @@ dens <- function(
 
   # applying filter to whole flowSet
 
-  result <- flowCore::filter(fsa, bacteria_gate)
+  result <- flowCore::filter(fsa, gates$bacteria$bacteria_gate)
 
   # extract absolute counts
   l <- lapply(result, flowCore::summary)
@@ -63,12 +63,12 @@ dens <- function(
   flow.data <- flow.data[order(flow.data$date, flow.data$sample_letter, flow.data$sample_number), ]
 
   # subset data based on gate for bacteria
-  subset.bacteria <- flowCore::Subset(fsa, bacteria_gate)
+  subset.bacteria <- flowCore::Subset(fsa, gates$bacteria$bacteria_gate)
 
   # applying filter to bacteria to get the three bacteria populations
-  LNA <- flowCore::filter(subset.bacteria, rg_LNA)
-  MNA <- flowCore::filter(subset.bacteria, rg_MNA)
-  HNA <- flowCore::filter(subset.bacteria, rg_HNA)
+  LNA <- flowCore::filter(subset.bacteria, gates$bacteria$rg_LNA)
+  MNA <- flowCore::filter(subset.bacteria, gates$bacteria$rg_MNA)
+  HNA <- flowCore::filter(subset.bacteria, gates$bacteria$rg_HNA)
 
   # extract absolute counts
   l_LNA <- lapply(LNA, flowCore::summary)
@@ -104,8 +104,8 @@ dens <- function(
 
   # get the algae
   algae <- flowCore::filter(
-    flowCore::Subset(fsa, !bacteria_gate),
-    algae_gate
+    flowCore::Subset(fsa, !gates$bacteria$bacteria_gate),
+    gates$algae$algae_gate
   )
 
   # extract absolute counts
diff --git a/R/dens_H.R b/R/dens_H.R
index fd63875..dc457d0 100644
--- a/R/dens_H.R
+++ b/R/dens_H.R
@@ -26,7 +26,7 @@ dens_H <- function(
   # #----- HAVING A LOOK AT THE GATING -----#
 
   # i <- 1
-  # flowViz::xyplot(`FL3-A` ~ `FL1-A`, data = fsa[[i]], filter = bacteria_gate)
+  # flowViz::xyplot(`FL3-A` ~ `FL1-A`, data = fsa[[i]], filter = gates$bacteria$bacteria_gate)
   # # fsa[[i]]
   # flowViz::densityplot(~ `FL1-A`, data = fsa[[i]], filter = rg_LNA)
   # # fsa[[i]]
@@ -42,7 +42,7 @@ dens_H <- function(
 
   # applying filter to whole flowSet
 
-  result <- flowCore::filter(fsa, bacteria_gate)
+  result <- flowCore::filter(fsa, gates$bacteria$gates$bacteria$bacteria_gate)
 
   # extract absolute counts
   l <- lapply(result, flowCore::summary)
@@ -63,7 +63,7 @@ dens_H <- function(
   flow.data <- flow.data[order(flow.data$date, flow.data$sample_letter, flow.data$sample_number), ]
 
   # subset data based on gate for bacteria
-  subset.bacteria <- flowCore::Subset(fsa, bacteria_gate)
+  subset.bacteria <- flowCore::Subset(fsa, gates$bacteria$bacteria_gate)
 
   # applying filter to bacteria to get the three bacteria populations
   LNA <- flowCore::filter(subset.bacteria, rg_LNA)
@@ -104,7 +104,7 @@ dens_H <- function(
 
   # get the algae
   algae <- flowCore::filter(
-    flowCore::Subset(fsa, !bacteria_gate),
+    flowCore::Subset(fsa, !gates$bacteria$bacteria_gate),
     algae_gate
   )
 
diff --git a/R/extract_traits.R b/R/extract_traits.R
new file mode 100644
index 0000000..5fb33fa
--- /dev/null
+++ b/R/extract_traits.R
@@ -0,0 +1,190 @@
+#' Extract flowcytometer traits
+#'
+#' NOT USED IN PIPLELINE!!!!
+#' This function is extracting data to be added to the database
+#' (and therefore make accessible for further analysis and forecasting)
+#' from \code{.fcs} files.
+#'
+#' @param input directory from which to read the data
+#' @param metadata_flowcytometer the content of the file
+#'   \code{metadata_flowcytometer.csv} which will be linked into the traits
+#' @param min_FSC.A numeric. If \code{!NULL}, \code{FSA.A <= min_FSC.A} will be fitered out by using
+#'   a rectangular filter
+#'   \code{flowCore::rectangleGate(filterId="filter_out_0", "FSC-A" = c(min_FSC.A, +Inf))}
+#' @param use_H if \code{TRUE}, gating will be done using \code{height},
+#'   otherwie \code{area}
+#' @param timestamp timestamp. Default: read from \code{sample_metadata.yml}
+#' @param fsa_p1 if \code{NULL}, \code{fsa_p1} will be read in, otherwise the
+#'   \code{fsa}
+#' @param fsa_p2 if \code{NULL}, \code{fsa_p2} will be read in, otherwise the
+#'   \code{fsa}
+#' @param gates_coordinates if \code{NULL}, \code{gates_coordinates} will be
+#'   read in, otherwise the \code{gates_coordinates}
+#' @param wellid_keyword the kwyword which is used to identify the well ID.
+#'   Usually "$WELLID" (default), but for the EAWAG Flowcytometer it is "$SMNO".
+#'
+#' @return invisibly \code{TRUE} when completed successful
+#'
+#' @importFrom flowCore read.flowSet pData phenoData exprs logTransform truncateTransform transform
+#' @importFrom flowCore rectangleGate polygonGate Subset
+#' @importFrom yaml read_yaml
+#' @importFrom stats setNames
+#' @importFrom utils read.csv write.csv
+#' @importFrom plyr join
+#' @importFrom tidyr pivot_longer
+#' @importFrom magrittr %>%
+#' @import loggit
+#' @export
+#'
+extract_traits <- function(
+    input = NULL,
+    particles = c("bacteria", "LNA", "MNA", "HNA", "algae"),
+    metadata_flowcytometer,
+    min_FSC.A = NULL,
+    use_H = FALSE,
+    timestamp = yaml::read_yaml(file.path(input, "sample_metadata.yml"))$timestamp,
+    fsa_p1 = NULL,
+    fsa_p2 = NULL,
+    gates_coordinates = NULL,
+    wellid_keyword = "$WELLID") {
+    message("   reading data  ...")
+
+    if (is.null(fsa_p1)) {
+        fsa_p1 <- readRDS(file = file.path(input, paste0("flowcytometer_fsa_ungated.p_1.rds")))
+    }
+
+    if (is.null(fsa_p2)) {
+        fsa_p2 <- readRDS(file = file.path(input, paste0("flowcytometer_fsa_ungated.p_1.rds")))
+    }
+
+    if (!is.null(min_FSC.A)) {
+        g0 <- flowCore::rectangleGate(filterId = "filter_out_0", "FSC-A" = c(min_FSC.A, +Inf))
+        fsa_p1 <- flowCore::Subset(fsa_p1, g0)
+        fsa_p2 <- flowCore::Subset(fsa_p2, g0)
+    }
+
+    if (is.null(gates_coordinates)) {
+        gates_coordinates <- utils::read.csv(file.path(input, "gates_coordinates.csv"))
+    }
+
+    if (use_H) {
+        gates <- calculate_gates_H(gates_coordinates = gates_coordinates)
+    } else {
+        gates <- calculate_gates(gates_coordinates = gates_coordinates)
+    }
+
+
+
+    # function to gate each plate ---------------------------------------------
+
+    trait_plate <- function(plate_id,
+                            fsa,
+                            gates = gates,
+                            wellid_keyword = wellid_keyword,
+                            timestamp = timestamp) {
+        # extraction function -----------------------------------------------------
+
+        extr_traits <- function(pop,
+                                wellid_keyword = wellid_keyword,
+                                timestamp = timestamp) {
+            traits <- flowCore::fsApply(
+                pop,
+                function(p) {
+                    result <- list()
+                    result$sample <- unlist(flowCore::keyword(p, wellid_keyword))
+                    result$plate <- plate_id
+                    x <- exprs(p)
+                    if (nrow(x) > 0) {
+                        result <- suppressWarnings(
+                            data.frame(
+                                result,
+                                x
+                            )
+                        )
+                    } else {
+                        result <- NULL
+                    }
+                    return(result)
+                }
+            )
+
+            traits <- do.call(rbind, traits)
+            traits$timestamp <- timestamp
+            return(traits)
+        }
+
+        traits <- list()
+        # The Bacteria ------------------------------------------------------------
+
+        bacteria_pop <- Subset(fsa, gates$bacteria$bacteria_gate)
+
+        # LNA_pop <- Subset(bacteria_pop, gates$bacteria$rg_LNA)
+        # MNA_pop <- Subset(bacteria_pop, gates$bacteria$rg_MNA)
+        # HNA_pop <- Subset(bacteria_pop, gates$bacteria$rg_HNA)
+
+        traits$bacteria <- extr_traits(bacteria_pop, wellid_keyword = wellid_keyword, timestamp = timestamp)
+
+        # The Algae ---------------------------------------------------------------
+
+        algae_pop <- Subset(fsa, gates$algae$algae_gate)
+
+        traits$algae <- extr_traits(bacteria_pop, wellid_keyword = wellid_keyword, timestamp = timestamp)
+
+        return(traits)
+    }
+
+
+    # Do the trait extraction for all plates --------------------------------------------
+
+    p1 <- trait_plate(
+        plate_id = "p_1",
+        fsa = fsa_p1,
+        gates = gates,
+        timestamp = timestamp,
+        wellid_keyword = wellid_keyword
+    )
+    p2 <- trait_plate(
+        plate_id = "p_2",
+        fsa = fsa_p2,
+        gates = gates,
+        timestamp = timestamp,
+        wellid_keyword = wellid_keyword
+    )
+
+    traits <- list()
+
+    traits$bacteria <- rbind(
+        p1$bacteria,
+        p2$bacteria
+    )
+    traits$algae <- rbind(
+        p1$algae,
+        p2$algae
+    )
+
+    traits$bacteria <- merge(
+        traits$bacteria,
+        metadata_flowcytometer,
+        by.x = c("sample", "plate"),
+        by.y = c("sample", "plate"),
+        all.x = TRUE,
+        all.y = FALSE
+    )
+    traits$algae <- merge(
+        traits$algae,
+        metadata_flowcytometer,
+        by.x = c("sample", "plate"),
+        by.y = c("sample", "plate"),
+        all.x = TRUE,
+        all.y = FALSE
+    )
+
+
+
+    # Finalize ----------------------------------------------------------------
+
+    message("   done")
+    message("########################################################")
+
+    return(traits)
+}
diff --git a/R/extractor_flowcytometer_density.R b/R/extractor_flowcytometer_density.R
index 24b1f10..0468d14 100644
--- a/R/extractor_flowcytometer_density.R
+++ b/R/extractor_flowcytometer_density.R
@@ -61,38 +61,45 @@ extractor_flowcytometer_density <- function(
   #############################################################
   #############################################################
 
-  if (is.null(gates_coordinates)) {
-    gates_coordinates <- utils::read.csv(file.path(input, "flowcytometer", "gates_coordinates.csv"))
-  }
 
-  if (is.null(fsa)) {
-    fsa <- readRDS(file.path(output, "flowcytometer", "flowcytometer_fsa_ungated.rds"))
-  }
 
-  if (is.null(flow.data)) {
-    flow.data <- utils::read.csv(file.path(output, "flowcytometer", "flowcytometer_ungated.csv"))
-  }
 
   #############################################################
   #############################################################
 
   # function to gate each plate ---------------------------------------------
 
-  gate_plate <- function(plate,
-                         input,
-                         output,
-                         use_H) {
+  gate_plate <- function(
+      plate,
+      input,
+      output,
+      use_H,
+      gates_coordinates,
+      fsa = NULL,
+      flow.data = NULL) {
+    if (is.null(gates_coordinates)) {
+      gates_coordinates <- utils::read.csv(file.path(input, "flowcytometer", "gates_coordinates.csv"))
+    }
+
+    if (is.null(fsa)) {
+      fsa <- readRDS(file.path(output, "flowcytometer", paste0("flowcytometer_fsa_ungated.", plate, ".rds")))
+    }
+
+    if (is.null(flow.data)) {
+      flow.data <- readRDS(file.path(output, "flowcytometer", paste0("flowcytometer_ungated.", plate, ".rds")))
+    }
+
     if (use_H) {
       gated <- dens_H(
-        gates_coordinates = utils::read.csv(file.path(input, "flowcytometer", "gates_coordinates.csv")),
-        fsa = file.path(file.path(output, "flowcytometer"), paste0("flowcytometer_fsa_ungated.", plate, ".rds")),
-        flow.data = file.path(file.path(output, "flowcytometer"), paste0("flowcytometer_ungated.", plate, ".rds"))
+        gates_coordinates = gates_coordinates,
+        fsa = fsa,
+        flow.data = flow.data
       )
     } else {
       gated <- dens(
-        gates_coordinates = utils::read.csv(file.path(input, "flowcytometer", "gates_coordinates.csv")),
-        fsa = file.path(file.path(output, "flowcytometer"), paste0("flowcytometer_fsa_ungated.", plate, ".rds")),
-        flow.data = file.path(file.path(output, "flowcytometer"), paste0("flowcytometer_ungated.", plate, ".rds"))
+        gates_coordinates = gates_coordinates,
+        fsa = fsa,
+        flow.data = flow.data
       )
     }
     # SAVE --------------------------------------------------------------------
@@ -133,7 +140,11 @@ extractor_flowcytometer_density <- function(
     plates,
     gate_plate,
     input = input,
-    output = output
+    output = output,
+    use_H = use_H,
+    gates_coordinates,
+    fsa = fsa,
+    flow.data = flow.data
   )
 
   # Finalise ----------------------------------------------------------------
@@ -172,7 +183,12 @@ extractor_flowcytometer_density <- function(
   message("########################################################")
 
   if (dens_back) {
-    return(flow.data)
+    density <- NULL
+    for (plate in plates) {
+      fdp <- readRDS(file.path(add_path, paste0("flowcytometer_density.", plate, ".rds")))
+      density <- rbind(density, fdp)
+    }
+    return(density)
   } else {
     invisible(TRUE)
   }
diff --git a/R/extractor_traits.R b/R/extractor_traits.R
index 06792cc..6eb7b9d 100644
--- a/R/extractor_traits.R
+++ b/R/extractor_traits.R
@@ -33,7 +33,6 @@
 #' @importFrom plyr join
 #' @importFrom tidyr pivot_longer
 #' @importFrom magrittr %>%
-#' @import loggit
 #' @export
 #'
 extractor_traits <- function(input = NULL,
@@ -63,7 +62,7 @@ extractor_traits <- function(input = NULL,
     }
 
     if (is.null(gates_coordinates)) {
-        gates_coordinates <- utils::read.csv(file.path(input_dir, "gates_coordinates.csv"))
+        gates_coordinates <- utils::read.csv(file.path(input, "gates_coordinates.csv"))
     }
 
     if (use_H) {
@@ -87,7 +86,7 @@ extractor_traits <- function(input = NULL,
                 pop,
                 function(p) {
                     result <- list()
-                    rresult$sample <- unlist(flowCore::keyword(p, wellid_keyword))
+                    result$sample <- unlist(flowCore::keyword(p, wellid_keyword))
                     result$plate <- plate_id
                     x <- exprs(p)
                     if (nrow(x) > 0) {
diff --git a/R/pre_processor_flowcytometer_c6.R b/R/pre_processor_flowcytometer_c6.R
index ce5ad1e..0d40a6b 100644
--- a/R/pre_processor_flowcytometer_c6.R
+++ b/R/pre_processor_flowcytometer_c6.R
@@ -18,7 +18,6 @@ pre_processor_flowcytometer_c6 <- function(
 ) {
   add_path <- file.path(output, "flowcytometer")
   dir.create(add_path, recursive = TRUE, showWarnings = FALSE)
-  loggit::set_logfile(file.path(add_path, "flowcytometer.log"))
 
   ##
   message("########################################################")
diff --git a/codemeta.json b/codemeta.json
index 5e6c4b5..23083b9 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -7,13 +7,13 @@
   "codeRepository": "https://github.com/LEEF-UZH/LEEF.measurement.flowcytometer",
   "issueTracker": "https://github.com/LEEF-UZH/LEEF.measurement.flowcytometer/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.9.5",
+  "version": "0.9.7",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.2.2 (2022-10-31)",
+  "runtimePlatform": "R version 4.3.1 (2023-06-16)",
   "author": [
     {
       "@type": "Person",
@@ -168,6 +168,6 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "82.183KB",
+  "fileSize": "0KB",
   "readme": "https://github.com/LEEF-UZH/LEEF.measurement.flowcytometer/blob/LEEF-2/Readme.md"
 }
diff --git a/man/calculate_gates.Rd b/man/calculate_gates.Rd
new file mode 100644
index 0000000..27c27f1
--- /dev/null
+++ b/man/calculate_gates.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calculate_gates.R
+\name{calculate_gates}
+\alias{calculate_gates}
+\title{Calculate gates based on gate co-ordinates in csv file using \code{area}}
+\usage{
+calculate_gates(input_dir = NULL, gates_coordinates = NULL)
+}
+\arguments{
+\item{input_dir}{directory which contains the file \code{gates_coordinates.csv}}
+
+\item{gates_coordinates}{contains gate co-ordinates. If \code{NULL} *default)
+the gates cootdinates are read in from \code{input_dir}}
+}
+\value{
+\code{list} containing two objects: gates for bacteria and gates for algae
+}
+\description{
+Calculate gates based on gate co-ordinates in csv file using \code{area}
+}
diff --git a/man/calculate_gates_H.Rd b/man/calculate_gates_H.Rd
new file mode 100644
index 0000000..6ef5342
--- /dev/null
+++ b/man/calculate_gates_H.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calculate_gates_H.R
+\name{calculate_gates_H}
+\alias{calculate_gates_H}
+\title{Calculate gates based on gate co-ordinates in csv file using \code{area}}
+\usage{
+calculate_gates_H(input_dir = NULL, gates_coordinates = NULL)
+}
+\arguments{
+\item{input_dir}{directory which contains the file \code{gates_coordinates.csv}}
+
+\item{gates_coordinates}{contains gate co-ordinates. If \code{NULL} *default)
+the gates cootdinates are read in from \code{input_dir}}
+}
+\value{
+\code{list} containing two objects: gates for bacteria and gates for algae
+}
+\description{
+Calculate gates based on gate co-ordinates in csv file using \code{area}
+}
diff --git a/man/dens.Rd b/man/dens.Rd
new file mode 100644
index 0000000..529e508
--- /dev/null
+++ b/man/dens.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dens.R
+\name{dens}
+\alias{dens}
+\title{Get density using \code{area} for gating}
+\usage{
+dens(gates_coordinates, fsa, flow.data, min_FSC.A = 1e-10)
+}
+\arguments{
+\item{gates_coordinates}{gates co-ordinates as read from the file \code{gates_coordinates.csv}}
+
+\item{fsa}{as read from \code{flowcytometer_fsa_ungated.rds}}
+
+\item{flow.data}{as read from \code{flowcytometer_ungated.csv}}
+
+\item{min_FSC.A}{numeric. If \code{!NULL}, \code{FSA.A <= min_FSC.A} will be fitered out by using
+a rectangular filter
+\code{flowCore::rectangleGate(filterId="filter_out_0", "FSC-A" = c(min_FSC.A, +Inf))}}
+}
+\value{
+gated \code{flow.data} density as saved in \code{flowcytometer_density.csv} and actual gates used
+}
+\description{
+Get density using \code{area} for gating
+}
diff --git a/man/dens_H.Rd b/man/dens_H.Rd
new file mode 100644
index 0000000..99462f1
--- /dev/null
+++ b/man/dens_H.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dens_H.R
+\name{dens_H}
+\alias{dens_H}
+\title{Get density using \code{height} for gating}
+\usage{
+dens_H(gates_coordinates, fsa, flow.data, min_FSC.A = 1e-10)
+}
+\arguments{
+\item{gates_coordinates}{gates co-ordinates as read from the file \code{gates_coordinates.csv}}
+
+\item{fsa}{as read from \code{flowcytometer_fsa_ungated.rds}}
+
+\item{flow.data}{as read from \code{flowcytometer_ungated.csv}}
+
+\item{min_FSC.A}{numeric. If \code{!NULL}, \code{FSA.A <= min_FSC.A} will be fitered out by using
+a rectangular filter
+\code{flowCore::rectangleGate(filterId="filter_out_0", "FSC-A" = c(min_FSC.A, +Inf))}}
+}
+\value{
+gated \code{flow.data} density as saved in \code{flowcytometer_density.csv} and actual gates used
+}
+\description{
+Get density using \code{height} for gating
+}
diff --git a/man/extract_traits.Rd b/man/extract_traits.Rd
new file mode 100644
index 0000000..7a225c7
--- /dev/null
+++ b/man/extract_traits.Rd
@@ -0,0 +1,55 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/extract_traits.R
+\name{extract_traits}
+\alias{extract_traits}
+\title{Extract flowcytometer traits}
+\usage{
+extract_traits(
+  input = NULL,
+  particles = c("bacteria", "LNA", "MNA", "HNA", "algae"),
+  metadata_flowcytometer,
+  min_FSC.A = NULL,
+  use_H = FALSE,
+  timestamp = yaml::read_yaml(file.path(input, "sample_metadata.yml"))$timestamp,
+  fsa_p1 = NULL,
+  fsa_p2 = NULL,
+  gates_coordinates = NULL,
+  wellid_keyword = "$WELLID"
+)
+}
+\arguments{
+\item{input}{directory from which to read the data}
+
+\item{metadata_flowcytometer}{the content of the file
+\code{metadata_flowcytometer.csv} which will be linked into the traits}
+
+\item{min_FSC.A}{numeric. If \code{!NULL}, \code{FSA.A <= min_FSC.A} will be fitered out by using
+a rectangular filter
+\code{flowCore::rectangleGate(filterId="filter_out_0", "FSC-A" = c(min_FSC.A, +Inf))}}
+
+\item{use_H}{if \code{TRUE}, gating will be done using \code{height},
+otherwie \code{area}}
+
+\item{timestamp}{timestamp. Default: read from \code{sample_metadata.yml}}
+
+\item{fsa_p1}{if \code{NULL}, \code{fsa_p1} will be read in, otherwise the
+\code{fsa}}
+
+\item{fsa_p2}{if \code{NULL}, \code{fsa_p2} will be read in, otherwise the
+\code{fsa}}
+
+\item{gates_coordinates}{if \code{NULL}, \code{gates_coordinates} will be
+read in, otherwise the \code{gates_coordinates}}
+
+\item{wellid_keyword}{the kwyword which is used to identify the well ID.
+Usually "$WELLID" (default), but for the EAWAG Flowcytometer it is "$SMNO".}
+}
+\value{
+invisibly \code{TRUE} when completed successful
+}
+\description{
+NOT USED IN PIPLELINE!!!!
+This function is extracting data to be added to the database
+(and therefore make accessible for further analysis and forecasting)
+from \code{.fcs} files.
+}
diff --git a/man/extractor_flowcytometer_gating.Rd b/man/extractor_flowcytometer_density.Rd
similarity index 57%
rename from man/extractor_flowcytometer_gating.Rd
rename to man/extractor_flowcytometer_density.Rd
index 3603391..b417c3c 100644
--- a/man/extractor_flowcytometer_gating.Rd
+++ b/man/extractor_flowcytometer_density.Rd
@@ -1,10 +1,19 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/extractor_flowcytometer_gating.R
-\name{extractor_flowcytometer_gating}
-\alias{extractor_flowcytometer_gating}
+% Please edit documentation in R/extractor_flowcytometer_density.R
+\name{extractor_flowcytometer_density}
+\alias{extractor_flowcytometer_density}
 \title{Extractor flowcytometer data}
 \usage{
-extractor_flowcytometer_gating(input, output)
+extractor_flowcytometer_density(
+  input = NA,
+  output = ".",
+  min_FSC.A = NULL,
+  use_H = FALSE,
+  gates_coordinates = NULL,
+  fsa = NULL,
+  flow.data = NULL,
+  dens_back = FALSE
+)
 }
 \arguments{
 \item{input}{directory from which to read the data}
diff --git a/man/extractor_traits.Rd b/man/extractor_traits.Rd
new file mode 100644
index 0000000..b278ec1
--- /dev/null
+++ b/man/extractor_traits.Rd
@@ -0,0 +1,54 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/extractor_traits.R
+\name{extractor_traits}
+\alias{extractor_traits}
+\title{Extractor flowcytometer data}
+\usage{
+extractor_traits(
+  input = NULL,
+  particles = c("bacteria", "LNA", "MNA", "HNA", "algae"),
+  metadata_flowcytometer,
+  min_FSC.A = NULL,
+  use_H = FALSE,
+  timestamp = yaml::read_yaml(file.path(input, "sample_metadata.yml"))$timestamp,
+  fsa_p1 = NULL,
+  fsa_p2 = NULL,
+  gates_coordinates = NULL,
+  wellid_keyword = "$WELLID"
+)
+}
+\arguments{
+\item{input}{directory from which to read the data}
+
+\item{metadata_flowcytometer}{the content of the file
+\code{metadata_flowcytometer.csv} which will be linked into the traits}
+
+\item{min_FSC.A}{numeric. If \code{!NULL}, \code{FSA.A <= min_FSC.A} will be fitered out by using
+a rectangular filter
+\code{flowCore::rectangleGate(filterId="filter_out_0", "FSC-A" = c(min_FSC.A, +Inf))}}
+
+\item{use_H}{if \code{TRUE}, gating will be done using \code{height},
+otherwie \code{area}}
+
+\item{timestamp}{timestamp. Default: read from \code{sample_metadata.yml}}
+
+\item{fsa_p1}{if \code{NULL}, \code{fsa_p1} will be read in, otherwise the
+\code{fsa}}
+
+\item{fsa_p2}{if \code{NULL}, \code{fsa_p2} will be read in, otherwise the
+\code{fsa}}
+
+\item{gates_coordinates}{if \code{NULL}, \code{gates_coordinates} will be
+read in, otherwise the \code{gates_coordinates}}
+
+\item{wellid_keyword}{the kwyword which is used to identify the well ID.
+Usually "$WELLID" (default), but for the EAWAG Flowcytometer it is "$SMNO".}
+}
+\value{
+invisibly \code{TRUE} when completed successful
+}
+\description{
+This function is extracting data to be added to the database
+(and therefore make accessible for further analysis and forecasting)
+from \code{.fcs} files.
+}
diff --git a/man/gating.Rd b/man/gating.Rd
deleted file mode 100644
index 7b29b03..0000000
--- a/man/gating.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/gating.R
-\name{gating}
-\alias{gating}
-\title{Do the gating}
-\usage{
-gating(gates_coordinates, fsa, flow.data)
-}
-\arguments{
-\item{gates_coordinates}{gates co-ordinates as read from the file \code{gates_coordinates.csv}}
-
-\item{fsa}{as read from \code{flowcytometer_fsa_ungated.rds}}
-
-\item{flow.data}{as read from \code{flowcytometer_ungated.csv}}
-}
-\value{
-gated \code{flow.data} density as saved in \code{flowcytometer_density.csv} and actual gates used
-}
-\description{
-Do the gating
-}