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Update DOI in README #3

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df078c9
Update DOI in README
baiddd Jun 13, 2022
63599c9
Script for file size and loading time benchmark
baiddd Jun 13, 2022
6f7af9b
Update README.md
baiddd Jun 13, 2022
4a49e5a
Update README.md
chzchz Oct 6, 2022
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1 change: 1 addition & 0 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6576521.svg)](https://doi.org/10.5281/zenodo.6576521)
# The SMLM file format
#### A portable and extendable file format for storing and sharing localization microscopy data.

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84 changes: 84 additions & 0 deletions data/file_format_benchmark/README.md
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# Data used to compare file sizes and loading times
* ## The following 21 data sets were selected randomly:

|Samples |DOI|
|--------|:----|
|1-4|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507641.svg)](https://doi.org/10.5281/zenodo.5507641)|
|8,13|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507638.svg)](https://doi.org/10.5281/zenodo.5507638)|
|15|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507634.svg)](https://doi.org/10.5281/zenodo.5507634)|
|21|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507329.svg)](https://doi.org/10.5281/zenodo.5507329)|
|25, 27|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507053.svg)](https://doi.org/10.5281/zenodo.5507053)|
|34, 34-2|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507305.svg)](https://doi.org/10.5281/zenodo.5507305)|
|35, 39|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507605.svg)](https://doi.org/10.5281/zenodo.5507605)|
|42|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507679.svg)](https://doi.org/10.5281/zenodo.5507679)|
|51-53|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507826.svg)](https://doi.org/10.5281/zenodo.5507826)|
|57|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5507976.svg)](https://doi.org/10.5281/zenodo.5507976)|
|64|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5508212.svg)](https://doi.org/10.5281/zenodo.5508212)|
|69|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5508210.svg)](https://doi.org/10.5281/zenodo.5508210)|
|71,73,74|[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5508210.svg)](https://doi.org/10.5281/zenodo.5508210)|

* ## Under ThunderSTORM (version: [dev-2016-09-10-b1](https://github.com/zitmen/thunderstorm/releases/tag/dev-2016-09-10-b1)) folder, download SMLM File plugin (version: [v0.1.1](https://github.com/imodpasteur/smlm-file-format/releases/tag/v0.1.1))

You should see "SMLM File" option when you are importing and exporting with ThunderSTORM
![Capture du 2022-06-13 16-23-43](https://user-images.githubusercontent.com/56833522/173398651-c93f00a1-fdfd-40d3-8321-14ccd8db23f9.png)


* ## Download corresponded data
* ## In Fiji(ImageJ) run macro script to export __*.csv__ format to __*.smlm__ and __*.tsf__

```java
folder="Folder of downloaded data";
savefolder=folder;


list=getFileList(folder);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], ".csv")){

filename=folder+"/"+list[i];
savename=savefolder+"/"+list[i];
print(""+filename);
print(""+filename.substring(0,filename.length-4)+".csv");
run("Import results", "detectmeasurementprotocol=true filepath="+filename+" fileformat=[CSV (comma separated)] livepreview=true rawimagestack= startingframe=1 append=false");
run("Export results", "floatprecision=5 filepath="+savename.substring(0,savename.length-4)+".tsf fileformat=[Tagged spot file] sigma=true intensity=true chi2=true offset=true saveprotocol=false x=true y=true bkgstd=true id=true uncertainty=true frame=true detections=true");
run("Export results", "floatprecision=5 filepath="+savename.substring(0,savename.length-4)+".smlm fileformat=[SMLM File] sigma=true intensity=true chi2=true offset=true saveprotocol=false x=true y=true bkgstd=true id=true uncertainty=true frame=true detections=true");

run("Close All");
}

}
```

* ## Compute loading (import) time through ThunderStorm plugin

```java
folder="Folder of downloaded and converted data";
savefolder=folder;

run("Close All");
list=getFileList(folder);
print("CellName,CSV,TSF,SMLM(ms)");
for (i=0; i<list.length; i++) {
if (endsWith(list[i], ".csv")){

filename=folder+"/"+list[i];
savename=savefolder+"/"+list[i];
t0_tmp = getTime();
run("Import results", "detectmeasurementprotocol=true filepath="+filename+" fileformat=[CSV (comma separated)] livepreview=true rawimagestack= startingframe=1 append=false");
tcsv = getTime()-t0_tmp;
run("Close All");
//print("tsf");
t0_tmp = getTime();
run("Import results", "detectmeasurementprotocol=true filepath="+filename.substring(0,filename.length-4)+".tsf"+" fileformat=[Tagged spot file] livepreview=true rawimagestack= startingframe=1 append=false");
ttsf = getTime()-t0_tmp;
run("Close All");
//print("smlm");
t0_tmp = getTime();
run("Import results", "detectmeasurementprotocol=true filepath="+filename.substring(0,filename.length-4)+".smlm"+" fileformat=[SMLM File] livepreview=true rawimagestack= startingframe=1 append=false");
tsmlm = getTime()-t0_tmp;
IJ.log(""+list[i].substring(0,list[i].length-4)+","+tcsv+","+ttsf+","+tsmlm);
}

}

```