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RNA-FRETools / MASH-FRET

MATLAB package to analyze single-molecule FRET data
https://rna-fretools.github.io/MASH-FRET/
GNU General Public License v3.0
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Merging traces with Dynamic Background #136

Closed nsivan16 closed 1 month ago

nsivan16 commented 1 month ago

Describe the bug Once traces are merged with a dynamic background, they are no longer corrected for the dynamic background.

To Reproduce Steps to reproduce the behavior:

  1. Have different data sets corrected for dynamic background
  2. Merge
  3. See error

Error Code

Expected behavior Merging the traces with the corrected dynamic background

Screenshots Traces prior to merge --> with dynamic background correction image

Same trace after merging image

Project file(s) If applicable, send the .mash files concerned by the bug to melodiehadzic@protonmail.com.

Desktop (please complete the following information):

mca-sh commented 1 month ago

Hi Nirusan and thank you for the bug report and the .mash files.

Indeed, dynamic background correction was not retained after the merging process since the method is automatically reset to "Manual", where a single value is subtracted to the trajectory.

I tried to handle the bug by locking the background correction prior merging projects. This means that background is corrected before merging and can not be modified after merging (you will see, the edit fields are off-enabled). You can find the updated version here: https://github.com/RNA-FRETools/MASH-FRET/archive/refs/heads/master.zip

Please tell me is it works for you (I could not do it myself on your .mash files since I needed the associated video files as well).

Best, Mélodie

nsivan16 commented 1 month ago

Hi Mélodie,

Sorry for the delayed response. I’ve tested the new version. However, it only locks the background for the first channel (see green in pdf file) and not for all the traces. Therefore I’ve attached a file with some screenshot to show you the difference between the single and the merged files.

Best, Niru

From: Mélodie @.> Sent: Sunday, 21 July 2024 18:37 To: @.> Cc: Nirusan @.>; @.> Subject: Re: [RNA-FRETools/MASH-FRET] Merging traces with Dynamic Background (Issue #136)

Hi Nirusan and thank you for the bug report and the .mash files.

Indeed, dynamic background correction was not retained after the merging process since the method is automatically reset to "Manual", where a single value is subtracted to the trajectory.

I tried to handle the bug by locking the background correction prior merging projects. This means that background is corrected before merging and can not be modified after merging (you will see, the edit fields are off-enabled). You can find the updated version here: https://github.com/RNA-FRETools/MASH-FRET/archive/refs/heads/master.zip

Please tell me is it works for you (I could not do it myself on your .mash files since I needed the associated video files as well).

Best, Mélodie

— Reply to this email directly, view it on GitHubhttps://github.com/RNA-FRETools/MASH-FRET/issues/136#issuecomment-2241705767, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWWQ4BAEP46ZW4ZTKEBCMDZNPPAJAVCNFSM6AAAAABLAXVB2KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENBRG4YDKNZWG4. You are receiving this because you authored the thread.Message ID: @.***>

mca-sh commented 1 month ago

Hi Nirusan,

Thank you for the feedback. Unfortunately the attached files are not transmitted when the email exchange is mediated by Github. Can you either send me the files via the issue tracker of GitHub (#136) or via a brand new email to my address (melodiehadzic@protonmail.com)?

In any case, I was not able to reproduce the error with my own files. So for the moment I can only recommend to check that the dynamic background correction was applied to each of the trajectories and that intensity calculations were updated (press UPDATE ALL) prior merging.

Thank you, Mélodie

mca-sh commented 1 month ago

Hey Nirusan,

Thank you very much for all the files. I don't understand because from my side, dynamic background correction is preserved after merging the two files eSce_03_processed.mash and eSce_04_processed.mash.

Be sure to use the last version of MASH (here) and delete all older version from your computer, just in case.

This is the exact procedure I followed:

  1. open eSce_03_processed.mash and select the corresponding frame_t_0.ets file when requested
  2. in panel "Background correction" of module "Trace Processing", check that the checkboxes dynamic and apply are activated for each trace in the popup menu data
  3. press all in panel "Background correction" and then Apply in the popup window
  4. press UPDATE ALL to re-calculate all intensities
  5. repeat steps 1-4 with file eSce_04_processed.mash
  6. merge the two projects

I guess you followed a similar procedure, but something might be different since we do not obtain the same results! Can you do the exact same steps and tell me if it is working/not?

Thanx, Mélodie

mca-sh commented 1 month ago

You can find the successfully merged project here: merged_eSce_03_and_04_MH.zip Can you also try to open it in MASH and see if the background panel is correctly locked?

nsivan16 commented 1 month ago

Hi Mélodie,

I have deleted and downloaded the newest version of MASH. That helped. Thank you!

Best, Niru

From: Mélodie Hadzic @.> Sent: Tuesday, 6 August 2024 10:16 To: RNA-FRETools/MASH-FRET @.> Cc: Nirusan Sivanantharasa @.>; Author @.> Subject: Re: [RNA-FRETools/MASH-FRET] Merging traces with Dynamic Background (Issue #136)

Hey Nirusan,

Thank you very much for all the files. I don't understand because from my side, dynamic background correction is preserved after merging the two files eSce_03_processed.mash and eSce_04_processed.mash.

Be sure to use the last version of MASH (herehttps://github.com/RNA-FRETools/MASH-FRET/archive/refs/heads/master.zip) and delete all older version from your computer, just in case.

This is the exact procedure I followed:

  1. open eSce_03_processed.mash and select the corresponding frame_t_0.ets file when requested
  2. in panel "Background correction" of module "Trace Processing", check that the checkboxes dynamic and apply are activated for each trace in the popup menu data
  3. press all in panel "Background correction" and then Apply in the popup window
  4. press UPDATE ALL to re-calculate all intensities
  5. repeat steps 1-4 with file eSce_04_processed.mash
  6. merge the two projects

I guess you followed a similar procedure, but something might be different since we do not obtain the same results! Can you do the exact same steps and tell me if it is working/not?

Thanx, Mélodie

— Reply to this email directly, view it on GitHubhttps://github.com/RNA-FRETools/MASH-FRET/issues/136#issuecomment-2270661921, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAWWQ4BNKJ6WNKPOKZ4OLJDZQCA27AVCNFSM6AAAAABLAXVB2KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZQGY3DCOJSGE. You are receiving this because you authored the thread.Message ID: @.***>

mca-sh commented 1 month ago

Oh great! Then I will close the issue now. Do not hesitate to reopen it if you find another related bug.

Best, Mélodie