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VH-Lab / SRNeuronAnalysis

pyramidal neuron analysis code
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Documentation for Running on Data #1

Open ishaan-khurana opened 2 years ago

ishaan-khurana commented 2 years ago

Hi,

I am trying to use this for a different dataset. I cannot seem to find the main program to run the functions from nor can I find what files to use for the data.

Is there a chance you can help me out?

Best Ishaan Khurana Van Hooser Lab Undergraduate

SarahRichards1928 commented 2 years ago

Hi Ishaan,

The code is written in Python 2.7, which was the newest version of Python compatible with Knossos at the time that I wrote the code. I also personally like to use the PyCharm IDE for Python.

The code is written to parse Knossos annotation files, but could likely be adapted fairly easily to use any file type that provides the user with (X,Y,Z) coordinates for nodes.

I hope this helps! Please feel free to contact me if you have any more questions!

Thanks, Sarah

On Tue, Jul 19, 2022, 11:52 AM ishaan-khurana @.***> wrote:

Hi,

I am trying to use this for a different dataset. I cannot seem to find the main program to run the functions from nor can I find what files to use for the data.

Is there a chance you can help me out?

Best Ishaan Khurana Van Hooser Lab Undergraduate

— Reply to this email directly, view it on GitHub https://github.com/VH-Lab/SRNeuronAnalysis/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACUNYTM72SHUAZB5YO66OWTVU3FLXANCNFSM54APQLHA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

ishaan-khurana commented 2 years ago

Hi Sarah,

I am also hoping to know what order to run the programs. I cannot seem to find a program that calls all of the functions

Best, Ishaan K

SarahRichards1928 commented 2 years ago

Hi Ishaan,

Once you have you annotations ready (or ideally a small test batch), you'll run Neuron_Calc_Database. You'll be promoted to 'Input Data Path' to your annotations. This will create a table in a database containing your analyzed data. The README contains an example as well.

Thanks, Sarah

On Thu, Jul 21, 2022, 11:12 AM ishaan-khurana @.***> wrote:

Hi Sarah,

I am also hoping to know what order to run the programs. I cannot seem to find a program that calls all of the functions

Best, Ishaan K

— Reply to this email directly, view it on GitHub https://github.com/VH-Lab/SRNeuronAnalysis/issues/1#issuecomment-1191606183, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACUNYTOJWTNUG3EX7RS2MV3VVFSD5ANCNFSM54APQLHA . You are receiving this because you commented.Message ID: @.***>