dwaithe / fcs_scanning_correlator Goto Github PK

Hi Dominic,
I was thinking the following issues might help with the Scan software:

1. Possibility of fixing the autocorrelation curves to a specific zoom size once the zooming is done. At the moment I can zoom it however when i fit the data again it goes back to the initial state.
2. On selection of a specific pixel, it should demonstrate the autocorrelation curve for that pixel only. However it tends to display the ones preceding the particular selected pixel as well. For example, if there are 10 pixels and I want to have a look at the fitted 5th pixel, it should only display the fitting for 5th pixel. However, the software is displaying all the 5 from 1st to 5th (atleast in the preliminary fitting to check how the fit is behaving).
3. A scroll-bar for visualizing the sample names in data series (on the fit function window).
4. Possibility of selecting the specific pixel or data based on residuals.
5. Save option for the trimmed csv files (load scanning data window).
6. Possibility of saving red-flagged fitted data-series (the ones not passing the chi-square test) separately and also to exclude them from further analysis. One can then look at them separately later.

Cheers
Dilip

Hi Dominic,

when loading a two-channel file (lsm5 or tiff) into FoCuS_scan, I noticed that the counts per molecule (cpm (kHz)) in CH1 are corrupted. The brightness from the moment calculation (in CH0 and CH1) seems fine. The cpm in CH0 seems fine.

I believe this is just a small bug due to conversion from Hz to kHz or vice versa.
I guess the issue arises in the file "scorrelation_objects.py"
For CH0 you divide the raw counts by 1000:
Line 141: kcountCH0.append(kcount/1000)
Whereas for CH1 you don't:
Line 208: kcountCH1.append(kcount)

Overall, it seems that the cpm in CH1 are in Hz and not kHz which might be confusing and would be great to have fixed or indicated.

Many thanks and best wihses,
Falk

Pablo informed us that presumably Zeiss has stopped supporting the lsm format for the LSM 980 and right now the FCS acquisitions can only be saved as czi. Thus, it would be good to have a CZI import functionality.

Thanks to Christoph Gohlke there is a Python import library available https://pypi.org/project/czifile/
Also, there is a demo available for reading CZI and OMETIFF in Python by Zeiss directly and a imgfileutils.py by Zeiss with some helper functions

Hi @dwaithe,

Having an issue that when I load .ptu into either 1_15 and 1_16, the software immediately crashes and I get the following error messsage.

unicodedecodeerror 'utf-8' codec can't decode byte 0xb5 in position 38: invalid start byte

I don't get the error in 1_13.

Happy to provide an example file if you want. I've been trying with files from a Leica SP5 using Symphotime 2.4.4874.

Hi Dominic,

in the most recent version of FoCuS_scan the intensity data (count rates, time traces) are not displayed anymore in the left corner of the "Load and correlate Data" tab. See attached images below. It works fine with an older version (14_74) and does not work with the most recent release (15_95).

I tested this with single and dual colour sFCS files in .lsm5 and .tiff format. I am using the compiled version of the software on a Windows 10 machine.

Would be great to enable the preivew of the time traces again!

Best,
Falk

Here the exemplary screenshots:

Old version (14_74)

New version (15_95

)