LCI + ICC Plate Merger
This tool merges a live cell-imaged (LCI) plate and the same plate re-imaged after fixation (ICC) into one virtual HCS.ai plate folder that can be analyzed in InCarta. Images are matched by well and site; wells not imaged in both plates are left out. Fixed-plate channels are renumbered to follow the last LCI channel, and the plate's .jdce and image_metadata CSV are rebuilt so IN Carta sees every channel. TIFFs stay in their original source folders and are referenced by metadata, so no image files are duplicated. Source folders are only read, never changed. Use Chrome or Edge.
1Root folder
↺Merged plates already in this folder
Opening a plate only shows its alignment panel; nothing changes until you click Align and update plate. Or merge a new plate below.
2Pick the plates
3Channels
LCI channels keep their numbers. Fixed-plate channels continue from the last LCI channel, in their original order. A fixed-plate channel with the same filter as an LCI channel (e.g. a second DAPI) is unticked by default; tick it to keep both.
For wells: click or drag across wells to select them; click a row letter or column number to select that whole row or column. Grey wells do not have images in both plates. A dot marks wells already in the merged plate folder.
| Keep | Source | Original | In merged plate |
|---|
Wells to merge
4Create merged plate
Virtual merge: no TIFF images are copied. The merged plate contains rebuilt metadata that points to the original LCI and ICC images. You can select one well, several wells, or all eligible wells.
Plate_Merger.html inside the merged plate folder (or this page), choose the same root folder,
and click Open for alignment under “Merged plates already in this folder”.
5Align fixed channels to live DAPI (optional)
Open the merged plate in IN Carta first. If the fixed channels look shifted, come back and click Align and update plate. For every well and site, the fixed-plate DAPI is registered to the live DAPI. Every fixed-plate channel at that site is then moved by the same x/y shift and rewritten in the merged plate. Nothing happens until you click that button. Shifts are always applied to the original fixed images, so running it again or restoring never compounds.
Sites below the match score (too few matching nuclei), or whose shift is far from the rest of their well, use the well's median shift instead (or the plate's, if the well has too few good sites).
| Well | Site | Measured dx, dy | Score | Applied dx, dy | Source |
|---|