Extracting each push from IMD
Posted: Thu May 20, 2021 3:49 pm
Hi everyone, hope you are all staying safe
Bit of a weird question this, but has anyone looked at trying to extract individual push data from the IMD?
What I would like is to get a few thousand pushes, with the ion counts per channel, as a text file (or csv)
We have some samples where a metal is not retained in the cell very well, so shows a significant amount in solution between cells. Processing an IMD (using a CD marker to identify events), only gives us half the picture, and excludes the signal between cells. I'm worried that what we are seeing is just the metal in solution that happened to be passing at the same time as a cell, rather than the metal that is associated with the cell
I would like to see if individual push data could show us that there is, or isn't, a corresponding increase in metal signal during pushes containing a cell.
Reprocessing of the IMD within the Fluidigm software doesn't seem to be able to be granular enough to turn individual pushes into individual events. If it could export an FCS of single pushes as events, then plotting CDmarker ion-count vs time and overlaying metal ion-count might be a way I can correllate the two
I'm thinking that taking the rainplot and turning it into a csv file is what I need, but I don't know if there is a way of getting that out of the IMD
(and yes, I do realise its not going to be a small file!)
Hope this question makes sense!
Thanks
Richard
Bit of a weird question this, but has anyone looked at trying to extract individual push data from the IMD?
What I would like is to get a few thousand pushes, with the ion counts per channel, as a text file (or csv)
We have some samples where a metal is not retained in the cell very well, so shows a significant amount in solution between cells. Processing an IMD (using a CD marker to identify events), only gives us half the picture, and excludes the signal between cells. I'm worried that what we are seeing is just the metal in solution that happened to be passing at the same time as a cell, rather than the metal that is associated with the cell
I would like to see if individual push data could show us that there is, or isn't, a corresponding increase in metal signal during pushes containing a cell.
Reprocessing of the IMD within the Fluidigm software doesn't seem to be able to be granular enough to turn individual pushes into individual events. If it could export an FCS of single pushes as events, then plotting CDmarker ion-count vs time and overlaying metal ion-count might be a way I can correllate the two
I'm thinking that taking the rainplot and turning it into a csv file is what I need, but I don't know if there is a way of getting that out of the IMD
(and yes, I do realise its not going to be a small file!)
Hope this question makes sense!
Thanks
Richard