Custom Analysis Part 2 - veeninglab/BactMAP GitHub Wiki

Import data

In the folder “Fig5D-H” you can find the analysis of a 2 minute interval time-lapse movie. I used SuperSegger to track the cells and get the cell outlines, while I used iSBatch`s single-molecule biophysics imageJ plugin to track DnaX foci. To find more information on this dataset, check its documentation page.

Import the .TIF image stack

To import the image stack DnaX-GFP.TIF, use extr_OriginalStack(). Note that these files are all bigger than what we worked with before, this, for instance, is a time-lapse of 115 images.

To make sure R has enough memory to handle bigger datasets, it is recommended to restart your R session before loading. Check the section on dealing with larger datasets for this and other tips on working with heavier data when using BactMAP.

image_custom <- extr_OriginalStack("Fig5D-H/DnaX-GFP.tif")

Import the cell tracks and outlines

Use extr_SuperSeggerCells()$mesh to get the cell tracks and outlines.

extr_SuperSeggerCells() takes the cell masks of each individual cell from the cellxxxx.mat-files in the xy1//cell folder, and the cell properties (length, width, etc) from the corresponding clist. Note that below, I put “frames=1”. This is because this timelapse is taken on only one position, namely “xy1”. I set “timelapse=TRUE”.

cells_custom <- extr_SuperSeggerCells("Fig5D-H/supseg", frames=1, mag="100x_DVMolgen", startframe=1, timelapse=TRUE)$mesh

Check the content of the mesh file using summary(cells_custom) and View(cells_custom).

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:arrow_left: Custom Analysis Part 1: Before Getting Started	Custom Analysis Part 3: Filtering the Data :arrow_right: