Importing data using BactMAP

Data from segmentation programs

program	detects	function
Oufti	cell meshes spots objects genealogy	extr_Oufti()
SuperSegger	cell meshes spots genealogy	extr_SuperSeggerClist and extr_SuperSeggerCells
ObjectJ	cell bounding box	extr_ObjectJ()
Morphometrics	cell meshes objects	extr_Morphometrics()
MicrobeJ	cell meshes spots objects	extr_MicrobeJ()
Custom import from other program	cell meshes spots objects	extr_Meshes(), extr_Spots()

Data from spot detection

Now, only the peak fitter and tracker output data from ISBatch are standardly importable in BactMAP. Other spot tracking output can be imported from .CSV or .TXT using extr_Spots.

program	function:
ISBatch	extr_ISBatch()
custom import from other program	extr_Spots()

TIFF data

Uploading the raw tiff stacks can be useful for making kymographs or projections without doing spot or object detection first, or to check your segmentation/detection visually.

data type	function:
greyscale, single channel TIFF/TIF image or image stack	extr_OriginalStack