Semi-Automated Routines for Functional Image Analysis (SARFIA)

SARFIA has been developed for the analysis of functional fluorescence data, for instance recordings from cells labeled with fluorescent calcium indicators. However, it allows access to a variety of inbuilt and custom-written image processing functions.

Key features are image-based detection of structures of interest using the Laplace operator, determining the positions of units in a layered network, clustering algorithms to classify units with similar functional responses, and a database to store, exchange and analyse results across experiments. GUI access to a wide range of analysis functions for image stacks. Loaders for .lsm and .ome.tif files, as well as generic .tif files.

The custom image processing functions include thresholding based on the Laplace operator, filtering of 3D waves using principal component analysis (PCA), rotating functions, images/image stacks without interpolation, line scan analysis; Automated baseline detection, hierarchical clustering and bleach subtraction from fluorescence traces.

The package includes a manual describing the control panels and a help file that describes all functions in detail.

A scientific paper based on SARFIA has been published in J Neurosci Meth (2010) 188(1):141-50. Please cite this paper when publishing data analysed in SARFIA.


Project Details

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Current Project Release

Semi-Automated Routines for Functional Image Analysis (SARFIA) IGOR.7.00.x-1.09-A

Release File:
Version: IGOR.7.00.x-1.09-A
Version Date: Mon, 08/21/2017 - 07:01 am
Version Major: 1
Version Extra: A
Version Patch Level: 9
OS Compatibility: Mac-Intel Windows
Release Notes: Requires Igor Pro 7 or later.
For Igor 6.3 compatibility download SARFIA version 1.07.

This release contains a detailed help file, describing all functions and a manual describing the control panels. To install, unzip and copy the contents of User Procedures into the WaveMetrics>User Procedures folder, the contents of Igor Procedures into the WaveMetrics>Igor Procedures folder and the contents of Help Files into the WaveMetrics>Igor Help Files.

1.09: Multithreaded "RemoveROI" to speed up removal of small (or large) ROIs; Minor improvements.
1.08: Requires Igor Pro 7 or newer. Resolved an error with Igor Pro 7.04. Improved center of mass calculations when drawn ROI size is larger than the actual image feature. Added Center of mass for time series. Added ROIstats for time series and for 3D time series. 2D distance transform now uses faster WaveMetrics code (new feature in ImageTransform);
1.07: Added loader for .ome.tiff and .lsm files. Fixed a bug when >256 traces were isolated, #256 was identical to #0, #257 to #1, etc. Resolved a conflict with Neuromatic. Many minor bugfixes.
1.05: Added new function DistanceTransform to calculate the distance transform of a binary image. Added function PopCorrelate to calculate the normalized cross-covariance of traces in a a populationwave. Added function DrawCoMPositions to label the relative positions of centers of mass (rather than their number). Repaired functions to measure the relative positions in a structure ("IPLPosition"). Sped up function MultiROIStats. Image stacks with 3 layers will now be displayed as a grayscale stack rather than a RGB image. Improved automatic parameters for stack registration (added flag /PSTK when calling ImageRegistration). Updated manual and help file with new and missing functions.
1.04: Many minor updates. Updated manual and help files. Added support for the latest ScanImage versions (3.6). Added a method to analyse overlays (see help file).
1.03: Added thresholding based on the à trous wavelet transform and extraction of the timecourse of all pixels in a binary or MultiROI ROI mask. Added version information ("About") in the menu. Updated help files.
1.02A: Removed unnecessary includes from CustomStart.ipf, added a missing procedure file (Difference.ipf).
1.02: Fixed a bug in the LoadMovie operation that would not load images with a single frame.
1.01: Added Manual; Minor bugfixes.
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