IRF-read should handle *.asc files

[JenuC]

IRF -expected file should be a 1-dimensional ASCII file (T-axis). unless there is a reason. Not all IRF are sdt files. Conventionally its tab-delimited *.asc file.

[Xanthorapedia]

This can be addressed in future development. The current system sees transients as coming from datasets and it takes some effort to adapt it to single transients.

[JenuC]

Most IRF that we handle in TCSPC labs are *.asc files. IRF-sdt is only an acquisition unit. One uses a single-pixel time-curve as IRF and not the whole image. This is because IRF is not distributed equally in an image. An image with urea crystal may have only 1 pixel that is from SHG and that is why I think we should handle .asc files ( even "instead" of sdt files).

[Xanthorapedia]

Are .asc files coming from raw .sdt's? The UI allows you to select a single pixel from a .sdt file as the IRF. Is that sufficient? Or are you suggesting that the acquisition unit is doing the work and generating the .asc file?

[JenuC]

a) .asc file is just one-pixel time-curve written in ascii format. It is easy to modify on a notepad and is derived from the acquisition software(either SPCM or SPCimage).
b) Maybe I can retry this on the UI after the manual is ready. I couldn't find a way to assign a single pixel for IRF. Maybe we should optionally display IRF with the fit so that the relative IRF position and shape can be evaluated before fitting dataset.
c)The common format of handling IRF is as a single time curve than sdt file for SPCImage. Users can generate that during acquisition or on the FLIMJ UI as you suggest. But the .asc file should be saved so that it can be loaded at a later stage (instead of the full sdt).

[JenuC]

@Xanthorapedia please upload/send_me an example *.asc file you used for enabling this feature. I can't make it work yet. Find attached a sample IRF ASCII file I used.
IRF.txt

[JenuC]

I tried a single T-axis, tab-delimited transposed axis, and a few others. nothing worked out. maybe refer to this site: https://www.becker-hickl.com/faq/how-to-use-a-measured-irf-in-flim-analysis-in-spcimage/

[Xanthorapedia]

Just a single list of photon counts delimited by whitespace (space, tab, newline, etc.) like in their example should work. Are you on the newest version?

Your IRF should look like this if you remove the time column:

[JenuC]

@Xanthorapedia : I like the way it looks. But please send me the modified file you used, so that I can test it on my end. It seems like I am missing something. My flimj-UI is current according to the FLIMJ-update site. Is there a different version on GitHub that I should try for this?

[JenuC]

I just tried with the flimj-ui-1,0.7 version on github. but i can't make the asc-loading to work. I tried with single column files with newline and whitespace separation. There is no error. i don't see the irf peak. that's all. I guess it would be easier for me if you could just send me the format that worked for you. at least i can rule out the file-format issue

[Xanthorapedia]

Can you try this one? Make sure your file has .asc as extension and select "Show IRF Intensity" option.

[JenuC]

okay. so it was not the file format. it was the secret "show-irf- intensity" dropdown menu. But now, I cannot see the IRF when the data file is loaded. I need to optimize the vertical bars/ fitting range based on where my IRF peak is. how can we fix that?

[Xanthorapedia]

The secret dropdown is documented in the manual. The default behavior is that if the IRF loading goes wrong, The error will be reported in the debug console. One improvement could be to automatically jump to "IRF Intensity" once an IRF is set. Shall we take that?

As for manually setting the ranges, any idea as to how to detect the peak boundary?