Short Description

Intensity projection along depth or time with multiple algorithms: mean, max, median, variance, standard deviation, saturated sum. Projection can be restricted to ROI.

Team: Bio Image Analysis
Institution: Institut Pasteur
Website: http://icy.bioimageanalysis.org

Documentation

This plug-in performs various types of intensity projections along depth (for 3D data) or time (for timelapse data).

The principle of intensity projection is to project all slices (or time frames) of a sequence into a single 2D image. Each pixel of this final image is therefore a combination of all pixels with the same 2D coordinates in every projected image. The way theses pixel values are combined is determined by the selected algorithm.

5 projection algorithms are currently available, with a screenshot of what they produce on a sample (3D) data set (The brightness/contrast has been adjusted for purpose of demonstration, with the careful attempt of not saturating the final screenshot). Images used here are courtesy of Romain Thibeaux and Nancy Guillén (Institut Pasteur), and are not usable for reproduction without prior authorization.

First, here is one slice of the original 3D dataset. You won’t see much, as it’s pretty thick. That’s just what we need to try out the various projection algorithms.

Original slice of a 3D dataset

  • Maximum Intensity Projection (a.k.a. MIP): 
    Each final projected pixel contains the maximum value of all pixels of same 2D coordinates in the original data. This algorithm is highly popular in 3D data visualization, as it gives a nice 2D glimpse of a potentially large data set. Note however that this algorithm has several issues: a) on an otherwise dark background, a single bright pixel that is due to imaging artifacts may appear in the final projection while it may not correspond to relevant information; b) on saturated data sets, the projection becomes less relevant, as it ends up mostly… saturated!

Maximum intensity projection

  • Mean Intensity Projection: 
    Instead of the maximum above, each pixel holds the average value of all equivalent pixels in the data set. This algorithm is rarely used, as the information gets both dimmed and blurred (similar to a large mean filter along the projection axis). While this is good to remove the background noise, the structures of interest suffer as well.

Mean intensity projection

  • Median Intensity Projection: 
    Same as the mean above, except the average value is replaced by the median, with even stronger dimming and blurring effects (small structures of interest are considered as background noise, and therefore are entirely removed). Note that this projection does provide an efficient way to estimate the overall background.

Median intensity projection

  • Standard Deviation Intensity Projection: 
    If you are at times dissatisfied with the maximum projection, try this one out. The standard deviation measure solves many of the previous issues: a) unlike the maximum (which select a single value), the standard deviation incorporates data from all slices/frames, and therefore handles saturated data pretty well (inner structures become visible again); b) by definition, the standard deviation does not average the data, it actually indicates the constrast variability across the data set, which is what we expect from a projected view after all.

Standard Deviation Intensity Projection

  • Saturated Sum:
    Summing all pixel values usually has little interest (it quickly ends up saturating the resulting projection), this algorithm gives the same color dynamic as the mean projection on non-saturated projections. What’s the point then? Well the idea is that saturation here won’t necessary occur in every pixel, so there are regions where some details can be enhanced, notably in dim areas where the mean projection can’t help.

Saturated Sum Intensity Projection

Resources needing this

7 reviews on “Intensity Projection

  1. Why not a Minimum projection ? Already done at light speed .... Just Perfect !!!

Leave a Review

Leave a review
Cancel review
View full changelog
Close changelog

Changelog

  • Version 1.6.1.0 • Released on: 2019-10-24 13:00:00
    Download
    Description:

    Small optimization for faster processing (last changes for volatile mode compatibility made the plugin much slower to process the intensity projection).

  • Version 1.6.0.0 • Released on: 2019-02-01 12:46:51
    Download
    Description:

    Updated to be compatible with volatile Sequence (Icy 2.0)

  • Version 1.5.3.1 • Released on: 2019-02-01 12:46:32
    Download
    Description:

    Updated to be compatible with volatile Sequence (Icy 2.0)

  • Version 1.5.3.0 • Released on: 2016-12-11 15:56:56
    Download
    Description:

    Added static access to a method

  • Version 1.5.2.0 • Released on: 2016-03-24 15:34:18
    Download
    Description:

    Fixed an issue where the histogram bounds were not properly updated on the projected data

  • Version 1.5.1.0 • Released on: 2016-02-11 10:49:02
    Download
    Description:

    Added a stop button

  • Version 1.5.0.1 • Released on: 2016-01-12 16:15:39
    Download
    Description:

    Re-uploaded .jar file

  • Version 1.5.0.0 • Released on: 2015-12-14 11:58:21
    Download
    Description:

    * Drastically improved performance on single-channel single-time point data
    * Changed methods to static access (for simpler script access)
    * Fixed color map assignment

  • Version 1.4.0.0 • Released on: 2013-12-12 18:58:57
    Download
    Description:

    New: Minimum intensity projection

  • Version 1.3.1.0 • Released on: 2013-11-08 13:31:04
    Download
    Description:

    Fixed an issue in metadata creation

  • Version 1.3.0.0 • Released on: 2013-11-02 15:04:12
    Download
    Description:

    * Updated to Icy 1.4.0.0
    * Metadata is now conserved in the projected data

  • Version 1.2.1.0 • Released on: 2013-08-20 15:53:56
    Download
    Description:

    Minor update: restriction to the sequence ROI is not applied if no ROI are present in the sequence.

  • Version 1.2.0.0 • Released on: 2013-08-20 15:43:40
    Download
    Description:

    New feature: projection can now be restricted to the sequence ROI

    Many thanks to Davide Heller for the suggestion.

  • Version 1.1.0.1 • Released on: 2012-10-30 10:20:09
    Download
    Description:

    Fixed minimum required kernel version

  • Version 1.1.0.0 • Released on: 2012-10-30 09:33:06
    Download
    Description:

    New: block implementation for protocols

  • Version 1.0.0.2 • Released on: 2012-02-20 13:16:25
    Download
    Description:

    Updated to EzPlug 1.6.4.1

  • Version 1.0.0.1 • Released on: 2011-07-20 17:19:58
    Download
    Description:

    adjusted classpath

  • Version 1.0.0.0 • Released on: 2011-07-20 17:13:35
    Download