Thadeo - In the end, you'll get what you pay for.  There are programs such as Weasel, but they are really very rudimentary and you're not likely to have it perform the work you're proposing in your list of needed capabilities.  I am not familiar with any free software that meets your requirements.  You should talk to your administrators about how to finance FlowJo or similar code with multiple users in your group.  Good luck, but you'll probably not find what you want for free.

Greetings.

In agreement with previous speeche, you'll probably not find a free software for accurate flow cytometry analysis. Moreover, you have to consider that when you publish your results in the materials and methods section you must be very careful and you have to present data that has been processed with accurate and detailed software.

Best regards

Dear Mr Trivilegio,

I use Flowing Software (http://www.uskonaskel.fi/flowingsoftware/) for data analysis. This software is free of charge and matches nearly all your requests.

Hope this helps.

If you need to do back-gating, you cannot use any other software than BD, because they have it patented.

Maybe one of these can help you?: http://www.cyto.purdue.edu/flowcyt/software/Catalog.htm

I used to use FlowJo, but I have recently discovered Flowing Software (also suggested by Svetlana) and it works perfectly! It is intuitive and easy to use. Only shame it doesn't work on mac.

http://www.uskonaskel.fi/flowingsoftware/

Thanks alot for big help using this software, I can transform my FACS link files from my machine itself that caused me longtime big headache after they claimed it's a versatile software presently installed in my machine but for business seek they wanted money out of this software. So in my own status as med user or technologist, why i will pay if everyone can share the free link. Thank a lot really appreciate .

Hi, You can check if cytofkit, cytofWorkflow, SPADE and flowCore Bioconductor packages in R environment satisfy your needs:

https://bioconductor.org/packages/release/bioc/html/cytofkit.html

https://www.bioconductor.org/packages//2.12/bioc/html/spade.html

https://bioconductor.org/packages/release/workflows/html/cytofWorkflow.html

https://bioconductor.org/packages/release/bioc/html/flowCore.html

You can also refer to this article:

Article CyTOF workflow: Differential discovery in high-throughput hi...

and check this discussion:

https://www.researchgate.net/post/algorithm_for_automated_flow_cytometry_analysis_using_R_language