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Updated with link to wiki
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ggirelli committed May 17, 2019
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3. <u>Hover</u> over a spectrum to visualize a short description below this paragraph.
4. <u>Click</u> 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)!

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