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SchapiroLabor / histoCAT

Histology Topography Cytometry Analysis Toolbox
https://SchapiroLabor.github.io/histoCAT/
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FCS Export #12

Open TIJohnson1 opened 5 years ago

TIJohnson1 commented 5 years ago

Hello,

The export fcs file option within histoCAT doesn't seem to be exporting the fcs files correctly in that they do not contain the different mass channels as parameters (please see attached document). I have previously done this successfully but now I am experiencing this issue even using data sets that previously exported fine. Is there something I am missing?

Any assistance would be greatly appreciated. FCS export issues.docx

DenisSch commented 5 years ago

Thank you for the report. Could you provide the following information: 1) What operating system are you using? 2) Which histoCAT version? Are you running it compiled or directly through MATLAB? 3) Could you upload an example sessionData and the corresponding fcs file.

Thank you!

DenisSch commented 5 years ago

I would like to follow up on the issue? Is this solved?

TIJohnson1 commented 5 years ago

Hi,

Thank you for your email and apologies for not responding sooner. I use Windows 10 and version 1.75 of histoCAT. I'm not 100% sure what you mean about compiled vs directly through MATLAB but I'm not using it through any program just straight from the exe file. I still have the issue but it seems more sporadic than I initially thought, sometimes the FCS export is working but other times not. I've seen the export work after opening the desktop shortcut of histoCAT vs the exe file in Program Files and also when I remove the image ID column from an exported csv file before dropping that file into FlowJo but not consistently meaning this doesn't seem to address the root cause.

I can upload some session data and the corresponding fcs file but I can have successful and unsuccessful fcs export using the same session data so I'm not sure how much it would inform us about the issue.

Best, Isaac

On Tue, 16 Oct 2018 at 16:48, DenisSch notifications@github.com wrote:

I would like to follow up on the issue? Is this solved?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BodenmillerGroup/histoCAT/issues/12#issuecomment-430290497, or mute the thread https://github.com/notifications/unsubscribe-auth/Ap0icOBJk0r1u69xNYWR_CITvjadjVZ_ks5ulf_JgaJpZM4XIMTX .

DenisSch commented 5 years ago

Dear Isaac,

Could you upload a session data and the corresponding corrupted fcs file(s)? Please let me know, if you find a reproducible minimal example in the meantime. It is very hard to reproduce the error otherwise.

Best

Denis

dtelad11 commented 5 years ago

Please see here:

https://github.com/RGLab/flowCore/issues/133

Could you address this in HistoCAT, please?

DenisSch commented 5 years ago

I will follow up on this with top-priority! Thank you!

dtelad11 commented 5 years ago

@DenisSch Thank you. You're welcome to email me at el.ad.david.amir@gmail.com if you need the FCS file.

DenisSch commented 5 years ago

I need the sessionData to reproduce this issues. Thank you!

arcolombo commented 5 years ago

@Isaac. You can run HistoCAT 2 ways, the first is issued within a matlab session. the second way is issued from a "stand alone" compiled version. if you have to open matlab to run histocat, then that is the 'matlab version'.