Analysis of time series data in CP 3.1.9

Dear all,
I am trying to use CP 3.1.9 to analyse data from a screen. With 4 time points.
Essentially for each field, i want to
i) generate a static ROI of cells if interest
ii) measure these cells across time.

The process so far
In Fiji

  • Merge timepoints into hyperstack.
    *Align images
    *Create Maximum projection
    *Save hyperstack and maximum projection

Cell profiler
-*Use Max proj to create masks of cells.

This is where i am stuck.
I can convert objects to an image and save this.

I can then create a new pipeline and load the images to be measured.
I can load the associated mask images and associate these with the correct image.
But I lose all the time points when I do this

How do i measure all time points within a given FOV with the same object ROIs?
One work around would be to just turn the ROI image into a stack with the right number of time points but i feel this is not the most sensible approach.

Many thanks for any help,

James

Hi,

Will you be able to share your pipeline or an screenshot of rhe problematic step. So that we could help you better. In the mean while check this link.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

Join us at, https://www.slas2020.org

Thanks Lakshmi,

The pipelines in the link are from an older version of CP and I have not found them helpful
I have made a work around by turning the ROI images into stacks.

Pipelines are TEst2_Projection.cpproj (1.0 MB)
This one takes a max projection and creates masks.
MeasureCells.cpproj (1.5 MB)
This one takes the masks and measures intensity over each frame

Hi @jimmib_78,

In one of your pipeline (for measuring) in NamesAndTypes for mask file you might have to change to none (refer to the screenshot here).

Also another which you could try is save your objects as mask in the previous pipeline by choosing “Binary” instead of Uni16. Later you could load as a object in the next pipeline. So you would mapping an object file with your time series image.
In case you face problem further, please share one of your time series with the mask.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

Join us at, https://www.slas2020.org