Pipeline for the mother machine


#1

Hello all!

I am at the university of pittsburgh doing research with a pdms microfluidic device commonly known as the `mother machine.’ For my research I am looking at the dynamics of a mother cell, trapped in each channel. I would like to measure an individual cell’s size, area and fluorescence. Seeing as the ‘mother machine’ is a rather popular device, I am wondering if anyone knows if there are pipelines in existence already that would suit my purposes.

Any help would be greatly appreciated,

Jeff


#2

Hi Jeff,

I don’t know of particular pipelines for this device, but if you care to post a couple pictures, it probably would be easy enough to generate a pipeline, especially for fluorescent cells.

Thanks,
David


#3

Hi David,

I thank you for the response. I have attached two images: one image is of the phase; the other image is of the fluorescence. For the purposes of my research, I need to be able to track the mother cell of the single trap displayed in the images attached (the cell on bottom in this case). every three minutes, a new image is taken and so the pipeline must be able to track this mother cell, measure its length, area and fluorescence.

Thanks again,

Jeff




#4

Hi,

I’m having a hard time making out where the cell is in these images. There is a bright single pixel toward the top of the fluorescent channel, but that seems too small. Or is the cell in the phase image, as the bright line, about 2-by-8 pixels wide? Is this a multiple exposure image? As you can tell, I am grasping at straws. Please can you annotate the images?

And when you say “track” we have a TrackObjects module to measure time-lapse style image stacks – is that what you mean, or do you simply want morphological measures for consecutive timepoints?

Thanks,
David


#5

Hi David,

I apologize that the images are not visible. I noticed that if you open these images with imagej, the images are much easier on the eyes than if you open it with your computer’s default image viewer. I hope that will help.

When I use the term ‘track’ I am meaning it to track an individual cell among other cells (in the pictures, the bottom, mother cell) for a series of time-lapse images. I wish to measure the size and area of the mother cell for each image in a stack of time-lapsed images. It sounds like the TrackModule will do for the tracking of a cell, but can it distinguish between different cells?

I very much appreciate the help,

Jeff


#6

Hi Jeff,

I can see the images (the attached screenshot is from FIJI), but I apparently don’t interpret them the way your expert eye does! I frankly don’t see much that looks like a cell – I see a bamboo like structure, i.e. a segmented line that is obviously the microfluidic channel. Can you please draw on the image (with Photoshop or Powerpoint, etc.) and show me what object you’d like to measure?
Also, are these single static images? In other words, what are the individual bright segments along the channel in the phase image (are they the same cell at different timepoints, or different cells, or what?

Thanks,
David


#7


Hi David,

My apologies again for the lack of clarity!! I have labelled the images to give the interpretation of the images. The image I have given you is a single image in time. In the phase image, the black dots are all different cells that have spawned from the bottom, mother cell. I wish to measure only the size, area and fluorescence of the bottom, mother cell. For the experiment I am working on, I take an image every three minutes. This is just one of many of the images I have taken. I am hoping that the TrackModule pipeline can locate the mother cell in each image and measure the length, area and fluorescence in each of the images.

I hope this provides the needed clarification. And thanks again,

Jeff