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Mariochem92 / PhasorIdentifier

Analyze fluorescence lifetime imaging FLIM files (.R64, .ref) effortlessly. Masking, cell segmentation, pH correlation, nanoscale effects, and precise quantification. Versatile for various research scenarios.
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Input file format #4

Open JoachimGoedhart opened 1 year ago

JoachimGoedhart commented 1 year ago

Fantastic work, I like where this is going! I am not familiar with the R64 format, it seems equipment specific? So my question would be whether you consider a more generalized input file format for FLIM data? We're currently using PicoQuant and Leica/Stellaris equipment for FLIM that both have the option to export data as .ptu So one suggestion would be to accept .ptu or perhaps provide some instructions of how to convert ptu into R64?

Cheers, Joachim.

Mariochem92 commented 1 year ago

Hello @JoachimGoedhart ! Thank you very much for your kind words and for opening the issue! I understand your concern regarding the script's equipment-specific nature. This is precisely why I envisioned this project as open-source, to enhance the analysis while making the code increasingly adaptable to different equipment and data formats.

To this end, I have recently been contributing to the PhasorPy library, and the community member there are actively working on an issue related to .ptu formats. You can find the .ptu file library under development by following this link.

If you have any FLIM data in .ptu format or any other format, I would greatly appreciate it if you could share it with us. As for Leica, what is the file format you are working with? For now as far as I understand you could save .ptu as .bin from PicoQuant software and convert it in SimFCS. But i can investigate this further if you need it :)

In closing, thank you again! Your input and testing would be invaluable as we work to make the analysis more versatile and accessible to researchers using different equipment and data formats.

Cheers, Mario

Mariochem92 commented 1 year ago

Here you can find also a comprehensive guide on how to convert the .ptu to .bin to readable data: Fit-free analysis of fluorescence lifetime imaging data using the phasor approach. In order to follow a fit-free procedure it is of utmost importance to collect also the signal of a calibration standard with mono exponential decay: possibly fluorescein.

JoachimGoedhart commented 1 year ago

Thanks for the reply and info, I will contact you over email to share a ptu file. We actually use .ptu files, as Leica has an export function for ptu.

Mariochem92 commented 1 year ago

Hi, thank you very much. I received the email!