From 2130713196fb7bc7de9c73e1cd8c0f10aae7fb61 Mon Sep 17 00:00:00 2001 From: Gabriele Girelli Date: Fri, 17 May 2019 16:09:24 +0200 Subject: [PATCH] Updated with link to wiki --- README.md | 63 +------------------------------------------------------ 1 file changed, 1 insertion(+), 62 deletions(-) diff --git a/README.md b/README.md index bef3d37..1d97abb 100644 --- a/README.md +++ b/README.md @@ -44,68 +44,7 @@ Usage 3. Hover over a spectrum to visualize a short description below this paragraph. 4. Click on a spectrum to visualize the raw data at the end of the page. -### How to add a new fluorophore - -You can add a new fluorophore in 2 easy steps: - -##### (1) Add the fluorophore's excitation/emission spectra - -Add the excitation and emission spectra to the `data/fluorophore-spectra` folder as tabulation-separated files (`.tsv`). The file name should be the fluorophore name followed by `_ex` or `_em`, respectively for excitation and emission spectra. For example, when adding the fluorophore `GFP`, two files should be added: `GFP_ex.tsv` and `GFP_em.tsv`. - -Each file should contain two columns (with a header line): - -* `w` is the wavelength in nanometers, -* and `ri` is the relative intensity in a.u.. Please, note that the relative intensity should be in the 0-1 range. - -Check out the examples available in the default installation [here](https://github.com/ggirelli/SpectraScope/tree/master/data/fluorophore-spectra). - -##### (2) Updated the main fluorophore table - -Update the `data/fluorophores.tsv` table by adding one line. The table contains 4 tabulation-separated columns: - -* `name` is the fluorophore name, -* `wex` is the wavelength (in nm) of the excitation peak, -* `wem` is the wavelength (in nm) of the emission peak, -* and `color` is either "auto" (in which case the color will be calculated based on `wem`; if `wem` is not in the visible range the automatic color will be "black") or an hexadecimal color string of your choice (useful when `wem` is outside the visible range). - -Check out the default fluorophores table [here](https://github.com/ggirelli/SpectraScope/blob/master/data/fluorophores.tsv)! In the case of EGFP, you would add a line like below: - -``` -EGFP 488 509 auto -``` - -### How to add a new filter - -You can add a new fluorophore 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 name. For example, when adding the filter `EM 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](https://github.com/ggirelli/SpectraScope/tree/master/data/filter-spectra). - -##### (2) Update the main filter table - -Update the `data/filters.tsv` table by adding one line. The table contains 7 tabulation-separated columns: - -* `name` is the fluorophore name, -* `producer` is the filter brand, -* `start` is the wavelength at which the transmittion window begins, -* `width` is the width (in nm) of the transmittion window, -* `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](https://github.com/ggirelli/SpectraScope/blob/master/data/filters.tsv)! In the case of the [Semrock FF605-Di02-25x36 filter](https://www.semrock.com/FilterDetails.aspx?id=FF605-Di02-25x36), you would add a line like below: - -``` -FF605-Di02 Semrock 605 Inf auto AF594 -``` +More info are available in our [Wiki](https://github.com/ggirelli/SpectraScope/wiki)! Contribute ---