extr_ObjectJ | R Documentation |
ObjectJ detects a bounding box around each cell, which it uses to calculate spot localization, cell width and cell length along the medial axis. It is possible to save the bounding box points manually by defining them in the Columns section of the ObjectJ results. Here you can download an ObjectJ Settings file where the bounding box columns are already created.
extr_ObjectJ( dataloc,
mag = "No_PixelCorrection",
boundingBoxX = c("X1", "X2", "X3", "X4", "X5",
"X6", "X7", "X8", "X9", "X10", "X11"),
boundingBoxY = c("Y1", "Y2", "Y3", "Y4", "Y5", "Y6",
"Y7", "Y8", "Y9", "Y10", "Y11"),
turn_meshes = TRUE,
cellList=FALSE)
dataloc |
The path to the saved .CSV or .TXT file from ObjectJ. |
mag |
Magnification conversion factor (see |
boundingBoxX |
The column names of the 11 X-coordinates of the bounding box of the cells. Put these columns in your ObjectJ analysis manually or download the ObjectJ Settings here. |
boundingBoxY |
The column names of the 11 Y-coordinates of the bounding box of the cells. Put these columns in your ObjectJ analysis manually or download the ObjectJ Settings here. |
turn_meshes |
Default TRUE. When TRUE, the bounding boxes are all turned so the mid-point is at [0,0] while the length axis of the cell is parallel to the X-axis. |
cellList |
Default FALSE. When TRUE, the "cellList" (see Values below) is part of the output. |
ObjectJ can already convert it's data to micron for you! Therefore, the default setting for "mag" is "no_PixelCorrection". Check what your settings are before converting the data using BactMAP.
$cellList |
The original CSV as dataframe. |
$mesh |
Dataframe containing the X and Y coordinates of the bounding box and cell dimensions. When |
GFPframe |
Dataset contains self-defined (by the user) fluorescence information from the ObjectJ eg septal position or fluorescence intensity. |
$chainframe |
Dataset contains information on cell chains: chain ID, length, width and if specified, fluorescence information. |
It is possible to define your own column names in ObjectJ - but (apart from the bounding box columns) bactMAP recognises the standard names only. See the [example objectJ settings file](https://github.com/vrrenske/bactMAPdata/blob/master/objectJ_settings.ojj) for the standard column names.
Renske van Raaphorst
https://sils.fnwi.uva.nl/bcb/objectj/
Vischer, Norbert OE, et al. "Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ." Frontiers in microbiology 6 (2015): 586.
## Not run:
#Take ObjectJ file interactively
#Using pipes:
library(tidyverse)
ObjectJ_output <- file.choose() %>% extr_ObjectJ()
#check summary
ObjectJ_output %>% summary()
#plot chain length distribution
ggplot(ObjectJ_output$chainframe, aes(x=ChainAxis)) + geom_histogram()
## End(Not run)
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