A Matlab application for processing and reviewing localization microscopy data.

rainSTORM v3.1.8 (2020. Jan) is stable, suggested for every day use, or try out the rainSTORM v4.0beta (2026. Jan).

rainSTORM v4.0beta (2026. Jan) is a new-beta release.

Based the “legacy” rainSTORM 3.x and the experimental “scripting version” codes.
The main aims of this release are to decrease the memory footprint and improve the reusability of codes and algorithms for custom analyss. For this purpose, it got a complete rewrite of the data handling.

• Release highlights:
  • General cleanup and rethink of many parts
  • Improved the reusability of algorithms by moving them into “libraries”
  • Easy custom analysis scripts creation
  • Most functionality can now be called via objects
  • Backward localization data compatibility (“rainSTORM legacy”). The “old” rainSTORM 3.x software is not compatible with the new data format!
  • The “rainSTORM” GUI software can no longer import csv data, this functionality moved to the “Image Viewer”
  • Image Viewer can be used separately (can import localization data saved in csv files)
  • Settings of the data processing can now be saved to and read from a json files, instead of being hardcoded in the code
  • Greatly reduced memory footprint of the loaded localization data (~20x decrease, as I recall)
  • New, more maintainable and more information rich format for the info file (JSON)
  • Support of localization data created with ThunderSTORM
  • Paved the way for the implementation of support of localization for data import/export of other algorithms
  • Ability to run ThunderSTORm via MIJ
  • Extraction of camera parameters from the image metadata instead of using predefines ones
  • Quasi-static flourescent background removal from he image stacks (by default, with moving median filtering)
  • Release of former experimental algorithms:
    • Astigmatic 3D
    • DBSCAN cluster analysis
    • Subsequent localization concatenation
  • Automatic contrast adjustment of the super-resolved image
  • Pixel size information is saved into the metadata of the super-resolved images and ImageJ can read this value
  • Colormap is saved into the super-resolved image tiff files, no need for separate colored png/jpeg images

rainSTORM v3.1.8 (2020. Jan) is an old-stable release.

• 2020. Jan update (v3.1.8): Bio Formats update to 6.3.1
• 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.
• 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.
• 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.
• 2017. December note: Works with R2018a.
• 2017. March update (v3.1.4): Quick fix for R2017a.
• 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.
• 2016. July updates (v3.1.1): Bridge tracker colourmap, minor filter range changes, rejected image viewing changes, experimental functions
• 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

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).
  • Required Toolboxes: Image Processing, Parallel Computing
• Run with: startup; rainSTORM;
• EOL 2017.01.01. Won’t recieve any updates.

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

Tested with Matlab R2014b-R2019a. Required Matlab Toolboxes:

• Required by main rainSTORM: Image Processing Toolbox
• Required by Auto Drift Correction: Optimization Toolbox
• Required to enable multi-threaded localization: Paralell Computing Toolbox

Run with: startup; rainSTORM;

Participation in SMLM Software Challenge 2016

User Guides for v3.1.*:

• rainSTORM_2016_user_guide_ver1 – User Guide version 1
• smlsm_2016_GT – poster presentation about using rainSTORM
• rainSTORM-blind-drift-correction – description of the auto drift correction algorithm

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.