3D volumes instead of 2d

[williamc96]

Hi Minxing Pang,

Do you have any advice for running this for 3d volumes instead of 2d images? I could run on each z-slice, but it would lose information across slices and would need to merge classes if it disagrees for the same cell across slices. Curious if you have thoughts about how to adapt this for 3d.

Thanks!
Will Cunningham

[maxpmx]

Hi Will,

Thank you for your interest in CelloType and your question about 3D volumes. While CelloType currently only supports 2D images, here are a few potential approaches you could consider:

1. Maximum Intensity Projection:

• Project the 3D volume into 2D using maximum intensity projection
• Run CelloType on the resulting 2D image
• This might work well if your cell features are clearly visible in the projection

2. Key z-slice selection:

• Select representative z-slices (e.g., where cells are in best focus)
• Process these key slices with CelloType
• This could work if your cells are well-represented in specific z-planes