Instrument Settings

wrmXpress can be used with a variety of data structures. Some pipelines require a particular structure - these requirements can be found in the relevant pipeline documentation. For more information, please see the data organization documentation.

Potential structures

ImageXpress + Single Well

  • Data is structured as TIFF files in TimePoint folders (see more).
  • Each TIFF image includes a single well.
  • Potential naming pattern:
    • {plate name}_{well}.TIF
    • {plate name}_{well}_{wavelength}.TIF

Examples:

96-well plate, 4X

TIFF, Single Site

96-well plate, 2X, Multi Wavelength

TIFF, Single Site TIFF, Single Site

ImageXpress + Multi Well

  • Data is structured as TIFF files in TimePoint folders (see more).
  • Each TIFF image includes more than 1 well.
  • Input the number of wells in each row/column of the image (integers).
  • For Plate format, input the total number of rows/cols on the plate

384-well plates

The Multi Well functionality is designed for 384-well plates. These have 24 columns and 16 wells, and imaging often occurs in 2 wells per row/column in each image.

ImageXpress + Multi Site

  • Data is structured as TIFF files in TimePoint folders (see more).
  • Each TIFF image includes a portion of a single well.
  • If the pipeline should first stitch the images together, select stitch. If the pipeline should analyze each site independently, leave it unselected.
  • Potential naming patterns:
    • {plate name}_{well}_{site}.TIF
    • {plate name}_{well}_{wavelength}_{site}.TIF

Examples:

Without stitching

TIFF, Single Site TIFF, Single Site

TIFF, Single Site TIFF, Single Site

With stitching

TIFF, Multi Site

AVI + Single Well

  • Videos are stored in AVI containers (see more).
  • Each AVI video includes a single well.
  • Potential naming patterns:
    • {plate name}_{well}.avi

Examples:

AVI, Single Well

AVI + Multi Well

  • Videos are stored in AVI containers (see more).
  • Each AVI video includes more than 1 well (i.e., an entire plate).
  • Set the Plate format to the true number of columns and rows (i.e., 12 and 8 or 6 and 4)
  • Set the Rows/Columns per image to 1
  • The Grid cropping option will split the video into a grid of rows and columns based on user input. More cropping options may be developed in the future.
    • For Grid cropping, it's important to pre-crop images so that the edges of the plate are removed. Grid cropping will simply crop equivalent rectangles based on the number of rows and columns.
  • Potential naming patterns:
    • {plate name}.avi

Examples:

96-well plate

AVI, Multi Well

24-well plate

AVI, Multi Well