The SMLM file format

A portable and extendable file format for storing and sharing localization microscopy data.

Key features

• lossless compression (using standard ZIP)
• smaller file size (convert a 7.2 GB .csv to 1.3 GB .smlm file)
• portable format (many tables in one file, supports multi-channel, tiled-acquisition etc.)
• fast loading time (fast transmission with small file size)
• easy to implement (provide examples in Javascript, Python, and Java)
• visualization with the web app (3D rendering, works for mobile devices, no installation required)
• flexible and extendable format (customized headers, formats)
• support meta information (store sample information in readable text format)
• fast preview with thumbnail support (thumbnail can be retrieved without unzipping the whole file)

ShareLoc Web App

You can now visualize your localization data with our ShareLoc Web App.

ShareLoc.xyz is a new website developed by us for promoting exchanging and sharing localization microscopy data. It consists of storage server which hold the publicly uploaded localization microscopy data, and a web application which allows easy sharing and visualization of the localization data, with only the browser.

With ShareLoc.xyz, you can share your localization data privately with others through an secured url, or upload your samples to our repository for public access.

For more detailed information about the platform, take a look at the ShareLoc source code.

ThunderSTORM Plugin

For supporting import and export as SMLM file format, we developed a ThunderSTORM Plugin which can be downloaded.

In order to make it work, you need to install the ThunderSTORM plugin first. Due to a change of plugin interface of ThunderSTORM, we had to release two different versions:

• If you use ThunderSTORM Version 1.3 and before, please install SMLM File plugin v0.1.0
• If you use the later versions of ThunderSTORM (e.g.: dev-2016-09-10-b1), please install SMLM File plugin v0.1.1.

Once you installed the SMLM file format plugin, you will be able to choose the "SMLM File" option when you are importing and exporting with ThunderSTORM. See here for more details about the plugin.

Benchmarks

We generated a localization table with 60,000 frames and ~47.8 million localizations from a DNA-PAINT experiment on mouse cells with Vimentin labeled. The table is generated from a ThunderSTROM plugin installed in Fiji. On the same computer (iMac 2017 with 3.4 GHz Intel Core i5, 32 GB memory), we first import the CSV file into ThunderSTROM and export it as TSF format. On the same computer, we import the same CSV file into our web app served on ShareLoc.xyz in a web browser(Chrome) and export the table as SMLM format. File size and loading time ware measured.

• (a) shows a comparison on the file size of these three different file formats. While the CSV file is 7,160 MB, and the TSF file is 2,610 MB, the corresponding SMLM file is 1,340 MB. Notice that although both CSV and TSF can be both zipped in order to achieve smaller file size, but their sizes are still much bigger than the SMLM file;

• (b) shows a comparison on loading time. Despite that the SMLM file has an additional decompression process compare to CSV and TSF, the loading time test shows it is still much faster to read. For files located on a local hard disk drive, the loading time are 466s, 191s and 79s for CSV, TSF and SMLM respectively.

• (c) illustrates how the file size changed during the two step compression in SMLM file format conversion. The CSV file is first converted to a binary file with 1,720 MB stored with float32 data type, and then zipped into a small SMLM file with 1,340 MB.

All the file formats and conversions are lossless, the content of the localization table are checked by comparing the consistency of rendered histogram images. The same experiment has been done with other data files which yields similar performance.

Update 1: With a recent improvement for handling large files, you can now load the smlm file on ShareLoc.xyz with all modern browsers including Chrome, Firefox and Safari.

For more detailed usage about ImJoy, go here.

Specification

Please go to the specification page.

Implemetations

The SMLM file format is designed to be easily implemented, to demonstrate that, we provide example implementations including in Javascript, Python and Java. Please find them in the implementations directory.

For using a small SMLM file, we compared the loading time with different implementation of the SMLM file format.

* The loading time of the Native Java implementation do not include the time for rendering histogram, and it was measured on a different computer. Fair comparisons will be provided sometime later.

Note: The performance of these implementations may be not optimal, they can be optimized further.

License

The specification and data are released under CC BY 4.0 license.

The implementations are released under MIT license.

Citation

This work is mainly supported by Institut Pasteur.

If you used it for a publication, please cite our paper Ouyang et al., Nat. Biotechnol. 2018, doi:10.1038/nbt.4106.