Serial sections of immunofluorescence

[gxygogogo]

Could this model be used to reconstruct a serial immunofluorescence sections?

[yyh030806]

Hi,
Thanks for your attention to our work and for the great question!

To clarify: immunofluorescence sections are pixel-level data — each image is essentially a matrix of pixel intensities across one or more fluorescence channels. DeepSpatial, however, operates at the single-cell level. Its input is a set of cells, where each cell is represented by its spatial coordinates, an expression vector, and a cell-type label. Because of this, DeepSpatial cannot be applied directly to raw immunofluorescence images for reconstruction.

That said, this is not a hard limitation. If you first perform cell segmentation on the fluorescence images (e.g., using tools such as Cellpose, Mesmer, or StarDist) to extract per-cell coordinates, channel intensities, and cell labels(optional), the resulting single-cell table can then be processed by DeepSpatial for 3D reconstruction.

Hope this helps, and please feel free to reach out if you have any further questions!

Best regards,
Yuhang Yang