rainSTORM v3_0A Matlab application for processing and reviewing localization microscopy data. (v3.0)

rainSTORM v2.37 is considered old-stable can be downloaded from the Laser Analytics Group site.

rainSTORM v3.0 (2015. Oct) is an old-stable release.

  • Release highlights:
    • new Graphical User Interface
    • new Multi Channel option
    • cleaned Workspace in Matlab
    • corrected background selection and subtraction
    • new file formats (e.g. nd2)
    • new Reporting tool (save reviewed data)
    • new Save Localizations tool (in csv)
    • new Bridge Tracker Tool
    • new Channel Merge Tool
    • new batch function for automated reviewing.
  • Tested with Matlab R2014a-R2016a (it might run on older versions).
  • Run with: startup; rainSTORM;
  • EOL 2017.01.01. Won’t recieve any updates.

rainSTORM v3.1.8 (2020. Jan) is stable, suggested for every day use.

  • 2016. May Release highlights v3.1:
    • new 2D Single-Gaussian Localization Algorithm
    • new 2D Multi-Gaussian Localization Algorithm
    • new background estimation methods (linear, constant)
    • updated Import and Export Super Resolution Parameters
    • updated Save & Load Sessions
    • new 2 Marker-Less Drift Correction Methods (Auto/Blind, BaSDI)
    • new/updated Histogram and Bridge Tracking Tools
  • 2016. July updates (v3.1.1): Bridge tracker colourmap, minor filter range changes, rejected image viewing changes, experimental functions
  • 2017. January updates (v3.1.3): Compatibility with Matlab R2016a & R2016b
    • R2016a/b: Fix a warning in rainSTORM_parfor_progress.
    • R2016b: Change how a colormap is applied on a super-resolved image.
  • 2017. March update (v3.1.4): Quick fix for R2017a.
  • 2017. December note: Works with R2018a.
  • 2018. January update (v3.1.5): Read single-frame tiff files in a folder.
    • new “tiff-folder” read method is introduced to handle single-frame tiff files in a folder. When using this method, keep every measurement in separate folders, and select the first image for a measurement in the file browser.
  • 2018. May update (v3.1.6): BioFormats update to 5.8.2.
    • NIS 5.0+ changes the nd2 file format a bit, thus an update is required.
  • 2019. May update (v3.1.7): Export select ROI feature
    • Backport ExportTracker tool to export localization data from selected ROIs on the Super-Resolution Image. IFM Analyser requires this feature.
    • Updated Auto Drift Algorithm with comments.
    • Removed the BaSDI Drift Correction button from the GUI, as it wasn’t as good as expected.
  • 2020. Jan update (v3.1.8): Bio Formats update to 6.3.1

Tested with Matlab R2014b-R2019a. Required Matlab Toolboxes:

Run with: startup; rainSTORM;

Participation in SMLM Software Challenge 2016

User Guides for v3.1.*:

rainSTORM v3.2 is under development, and is maintained at gitlab.com. To get involved or to be an early adopter, please contact Miklós Erdélyi for access.

Note#1: we keep only major versions, and any minor release overwrites the previous one.

Note#2 (2018.01.09.): After applying the Windows 10 security fix for the Meltdown issue rainSTORM localization took 11% longer on an i7-6700K CPU.


  1. […] the same file. Clearly there is bug somewhere, and as our localization and reconstruction software (rainSTORM) depends on BioFormats, a solution had to be found as I did not want to batch convert all files to […]