Tiff Images from Leica Stellaris

[rana228]

Hi,

I have Tiff images from Leica Stellaris Microscope and I was trying to generate cell masks using mesmer. But it doesn't generate any output or error. And I think there might be a issue with the panel as In Stellaris we use stains like dapi, dsRed etc instead of metal labelled antibodies. I don't know what information should I put in the panel file. Could you please help me out with this.

Thank you!! panel.csv

[Milad4849]

Hi @rana228,

Thank you for reaching out. For deepcell segmentation, the TIFFs need to be in a specific format. A deepcell column in the panel file is required, if the TIFFs are not already in the right format. Please refer to the relevant documentation here and here.

[rana228]

Hi @Milad4849,

Thank you for your quick response.

Actually, as you can see in the panel file, I have used Hoechst, DsRed and APC for staining. The Stellaris microscope generates 8-bit tiff images. As it's my first time using Steinbock for data from a microscope, I am not sure what information to put in the Panel file. I think my tif file is not compatible with deepcell as per the Steinbock documentation because it's 8-bit. Also by multi-channel image you mean all channels in a single image or separately inside the same input folder. Could you please guide me.

My main aim is to create a mask with APC and look at an overlay with DsRed channel. Are there any other options to achieve this?

Thank you for your time.

[Milad4849]

@rana228 Please refer at the documentation of steinbock, the panel file composition and your other inquiries are explained in detail there. I recommend going through the provided example to better understand the file formats and how steinbock works in general.

[Milad4849]

Closing due to inactivity