Closed nsivan16 closed 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
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: @.***>
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
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:
eSce_03_processed.mash
and select the corresponding frame_t_0.ets
file when requesteddynamic
and apply
are activated for each trace in the popup menu data
all
in panel "Background correction" and then Apply
in the popup windowUPDATE ALL
to re-calculate all intensitieseSce_04_processed.mash
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
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?
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:
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: @.***>
Oh great! Then I will close the issue now. Do not hesitate to reopen it if you find another related bug.
Best, Mélodie
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:
Error Code
Expected behavior Merging the traces with the corrected dynamic background
Screenshots Traces prior to merge --> with dynamic background correction![image](https://github.com/user-attachments/assets/4961c029-9d8f-4199-a49a-25536789d4dc)
Same trace after merging![image](https://github.com/user-attachments/assets/89db91d6-8c40-47f7-8117-3848e14f8460)
Project file(s) If applicable, send the
.mash
files concerned by the bug to melodiehadzic@protonmail.com.Desktop (please complete the following information):