add demo

[jxchen01]

demo 1 : how to create multi-channel image with proper meta data
demo 2: how to load metadata and use meta for different purpuses

[jxchen01]

@Dexnjn I have added a new folder in our shared drive, called "source_cut", This is just a temporay folder, if we all happy with this version, we can use this to replace the current "cut" folder and use it as the starting point of the pipeline. If we are not happy with it, we can still keep the old version.

I added a jupyter notebook to show (1) how I made these multi-channel images with proper metadata, (2) how to retrieve meta data and load a specific channel by name.

[Dexnjn]

Will users be forced to define the "physical_pixel_sizes" in the metadata or do we want to include the option to do it manually in the config as well?

[jxchen01]

Good questions. I think like what we usually do, we just check if physical pixel size is available in the meta data, if yes, use it, if no, check if users have set this in the config. How is that? I think this will be an easy implementation with good flexibility

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________________________________ From: Devon Siemes ***@***.***> Sent: Tuesday, March 21, 2023 3:31:50 PM To: MMV-Lab/immun_analysis ***@***.***> Cc: Jianxu Chen ***@***.***>; Author ***@***.***> Subject: Re: [MMV-Lab/immun_analysis] add demo (PR #4) Will users be forced to define the "physical_pixel_sizes" in the metadata or do we want to include the option to do it manually in the config as well? — Reply to this email directly, view it on GitHub<#4 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB3TAA7TMAFS67CJA6KOWLDW5G3VNANCNFSM6AAAAAAWCDXSKY>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[Dexnjn]

Adapted the workflow to support multi-channel inputs.
This also made some information easier to infer, i.e. exact filetypes etc.