AFid.qmd

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<h1 style="color: white; text-align:center;">AFid: A tool for automated identification and exclusion of autofluorescent objects from microscopy images </h1>
  	 
	 	<img src="images/AF/Heeva.gif" style="width: 100%; height: auto">
		 
		 <h2 style="color: white;"> About </h2>
		 Autofluorescence is a long-standing problem that has hindered fluorescence microscopy image analysis. To address this, we have developed a method that identifies autofluorescent signals from multi-channel images post acquisition. 
		 See the <u><b><a href="https://ellispatrick.github.io/AFid" target="_blank" style="color: white">gallery</a></b></u> for examples demonstrating the broad utility of this algorithm in accurately identifying and removing interfering autofluorescent signals.
		 You can find more information on how our tool works <u><b><a href="https://ellispatrick.github.io/AFid" target="_blank" style="color: white">here</a></b></u>.
		
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		<h2> Software </h2>
		For the benefit of the community we have made our autofluorescence identification tool and vignettes illustrating its use available for...

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    <th><b>FIJI:&nbsp;&nbsp;&nbsp;&nbsp;</b></th>
    <td><u><b><a href="https://github.com/ellispatrick/AFidImageJ" target="_blank" style="color: white">https://github.com/ellispatrick/AFidImageJ</a></b></u></td> 
	<th><b>&nbsp;&nbsp;&nbsp;&nbsp;[please use latest version of Fiji]</b></th>
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    <td><b>Matlab:&nbsp;&nbsp;&nbsp;&nbsp;</b></td>
   <td><u><b><a href="https://github.com/ellispatrick/AFidMatlab" target="_blank" style="color: white">https://github.com/ellispatrick/AFidMatlab</a></b></u></td> 
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    <td><b>R:&nbsp;&nbsp;&nbsp;&nbsp;</b></td>
    <td><u><b><a href="https://github.com/ellispatrick/AFidR" target="_blank" style="color: white">https://github.com/ellispatrick/AFidR</a></b></u></td> 
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		<h2 style="color: white;"> Citation </h2>
		
		We very much appreciate you referencing our work when you use it.
		
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		Baharlou H*, Canete, N*, Bertram KM, Sandgren KJ, Cunningham AL, Harman AN and Patrick E. (2021) AFid: a tool for automated identification and exclusion of autofluorescent objects from microscopy images <i> Bioinformatics</i> 
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		Raw data and scripts to reproduce the figures are available on <td><u><b><a href="https://zenodo.org/record/3898373#.Xuq-NkUvOUl" target="_blank" style="color: white">https://zenodo.org/record/3898373#.Xuq-NkUvOUl</a></b></u></td> 
		
		
		
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