November 29, 2019
How to Import to Screen mode using Columbus CSV Import Type.
If your instrument's file format is not included in Columbus's Screen mode Import Types you can attempt import by using the Columbus CSV Import Type.
In most circumstances you will have a collection of single image files such as TIFFs. To use the Columbus CSV Import Type you will need to create an index file, this instructs the Columbus importer on how to arrange the files in a Plate of a Screen. Download an example file here. This example includes a few sample images to show the file's arrangement.
- Add your file's details to the index file example.ColumbusIDX.csv to include Row, Column, Field etc. The example file contains the bare miniumum to import the files but other metdata columns can be included as required, a complete list can be found at the bottom of this note. If you choose to rename the file maintain the .ColumbusIDX.csv file ending. The SourceFilename requires the complete name of the file including any extensions, watch for any variations such as .tiff and .tif, names need to be exact.
- Move the index file to the path containing the images to be imported.
- In the Columbus Import dialog Set Import Type to Columbus CSV, select the path and other options as required.
The Compete list of Metadata is as follows:
- SourceImage - the binary image data
- Channel* - The channel counter (starting with 1)
- ChannelName - The name of the channel (e.g. Hoechst)
- ChannelType - The type of the channel (allowed Types: "Brightfield","Fluorescence")
- ChannelColor - The preferred color of the channel (e.g. "Blue", "#FF0000" or RGB tuple)
- MainExcitationWavelength@nm - The excitation color for the channel (e.g. 488 for wavelength in nm)
- MainEmissionWavelength@nm - The emission color for the channel (e.g. 488 for wavelength in nm)
- AcquisitionType - The acquistion type of the channel (allowed Types: "Confocal","NonConfocal", "nipkowconfocal" and OME Tiff Acquisition Type)
- Plane* - The plane counter (starting with 1; partly used as ID)
- Timepoint* - The timepoint counter (starting with 1; partly used as ID)
- ImageResolutionX@um - The width of a single pixel in micro meter, typically determined by Camera-Pixel-Size * Camera-Binning-X / Objective-Magnification
- ImageResolutionY@um - The height of a single pixel in micro meter, typically determined by Camera-Pixel-Size * Camera-Binning-Y / Objective-Magnification
- ImageResolutionZ@um - The height (z-dimension) of a single pixel in micro meter
- PositionX@um - The X distance from the center of the well in micro meter
- PositionY@um - The Y distance from the center of the well in micro meter
- PositionZ@um - The distance between the image acqusition height and the upper glass surface measured inmicro meter
- TimeOffset@s - The time difference between an arbitrary absolute time position and the acquisition time
- AbsoluteTime@s - The time absolute time as number of seconds since January 1, 1970, in UTC
- BufferNo -
- Row* - The row number of the well (starting with 1)
- Column* - The column number of the well (starting with 1)
- Field* - The field counter (starting with 1; partly used as ID)
- WellName - Excel style well name like (A4) (if given used as image name with trailing 'Field' counter)