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How to add a filter

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Gabriele Girelli edited this page May 29, 2019 · 3 revisions

You can add a new filter in 2 easy steps:

(1) Add the filter's transmission spectrum

Add the transmission spectrum to the data/filter-spectra folder as tabulation-separated files (.tsv). The file name should be the filter type and name, separated by a space. For example, when adding the emission (EM) filter FF001-625-20, the file should be named EM FF01-625-20.tsv.

The transmission spectrum file should contain two columns (with a header line):

  • w is the wavelength in nanometers,
  • and ri is the relative transmitted intensity in a.u.. Please, note that the relative transmitted intensity should be in the 0-1 range.

Check out the examples available in the default installation here.

(2) Update the main filter table

Update the data/filters.tsv table by adding one line. The table contains 7 tabulation-separated columns:

  • type is the filter type, which should be one of the following:
    • EX for excitation filters,
    • DM for dichroic mirrors,
    • EM for emission filters,
  • name is the filter name,
  • producer is the filter brand,
  • mid is the wavelength at the transmission window midpoint,
  • width is the width (in nm) of the transmission window (set this to none for dichroic mirrors),
  • scope is a comma-separated list of microscopes that have that filter set,
  • color is either "auto" (in which case the color will be calculated based on start; if start is not in the visible range the automatic color will be "black") or an hexadecimal color string of your choice (useful when start is outside the visible range),
  • nickname can be used to specify fluorophores compatible with the filters in a comma-separated fashion,
  • and customDescription can be used to write a short description that is then reported in the interface. If this column is left empty, then the description will be start/width.

Check out the default filters table here! In the case of the Semrock FF605-Di02-25x36 filter, you would add a line like below:

type	name	producer	mid	width	scope	color	nickname	customDescription
DM	FF605-Di02	Semrock	605	none	scope 1, scope 2	auto	AF594
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