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Feb 2011
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Dec 2018
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Short Description

Spot detector detects and counts spots.

– Detects spots in noisy images 2D/3D.
– Depending on objective, spots can be nuclei, nucleus or cell
– Versatile input: sequence or batch of file.
– Detects spot in specific band/channel.
– Multi band labeling: automaticaly creates ROIs from one band and count in the same or an other band.
– Filters detection by size.
– Sort detection by ROIs
– Output data in XLS Excel files: number of detection by ROIs, and each detection location and size.
– Outputs withness image with ROIs and detection painted on it.
– Outputs binary detection image.
– Displays detections
– Displays tags

Documentation

Setting up the processing pipeline

The detection process is divided in several sub processes

Input

The input can be the current sequence or a batch of file.

Pre processing

The pre processor is currently composed of only one module to select the desired channel to use for detection.

Detector

 

 

 

 

 

 

 

 

 

 

 

The UnDecimated Wavelet Transfrom detector is designed to detect spots, even if the amount of noise in the image is high.

You need to setup whereas the spot you wish to detect are brighter or darker than the background. As you select which option to use, an example of the image expected is displayed in the box bellow.

The panel size of spots to detect (scale and threshold) let you specify the size of the spot you wish to detect. Each scale correspond to a spot size. The scale 1 is very small and tends to extract the noise, and should not be used. The scale 2 (default) is often a good deal for spots of about 4 to 7 pixels diameter. Then, with the button add scale you can set bigger scales that will double the size of the object you wish to detect. Note that the use of too big scales (4 or 5) will tend to link detection between them.

In the detection process, original images are processed to obtain coefficient images (basically coefficient images contains the impulse response of a corresponding scale, with limited influence of the other scales, so typically it removes the background and the noise). In those images, a Wavelet Adaptive Threshold is computed. Then you can influence the automatic thresholding with the value you enter: If you leave the default 100 value, then you will obtain the set of detection found with the original WAT. If you set 80, you will obtain less detection. 140 is a very high value, you will have a lot of detection, and you should not go above except in very specific situations. Also, if your detection is too sensitive, this will connect detections. As they connect, you obtain less detection, even if you are more sensitive.

It is possible to combine several scale. If you do so, only the pixel present in each different scale will be kept for the final detection.

New: The option ‘consider WAT considering ROI’ has been introduced to help people taking images with either unregular background tissues or if large areas of saturated signal is present in the image (typically in the next image example below, the white area on the right hand side of the picture.). If enabled, the WAT is computed on the union of all the ROIs present in the image.

If the display binary image checkbox is selected, the program will display a black and white image representing the filtered output of the wavelet detection.

Region of Interest

ROI from sequence
The ROI drawn by the users are used by the detector. If no ROI is present, the whole image is considered. If one or more ROIs are presents, then the program only considers detections inside ROIs. The program recognize the black ROIs as removed area (could be scratches, destroyed tissue…). All results in the final Excel file will then be classified by ROI, providing its id, number of detection and its area in pixels² (see output section for details). Black ROIs are substracted to all other presents ROIs.

ROI from band
In the following image, the user wishes to detect the red spots, but only if they are over the blue area. This module let the user choose which channel to use as a driver channel, and creates an ROI to use for the detection.

 

 

 

 

 

 

 

The parameters are the band/channel number, and the threshold to apply. Settings can be tested directly on the current sequence selected.

If the checkbox enable multiple ROIs is selected, then each cell will be individualy segmented. A size criteria (Minimum size of ROI) is used to avoid segmenting the too little cells.

The two following images illustrates the automatic segmentation of the cell, and then the automatic count in red channel for each cell:

Filtering

The current filtering box is very simple and only provide a size criteria.

 

 

 

 

 

 

 

 

 

 

Output

The output exports detection data to Excel, and also provides images with detection markers and binary image for control.

By default all the outputs are stored in a folder named save located in the same folder as the input images. If you run several times the detector, the image and XLS file in the save folder will be overwritten.

If you use the option append data to existing files, the XLS file will get an extra datesheet per detection process.This could lead to very big file.

You can also centralize all results to one file using the enable specific file option. Several mode can be used at the same time: automatic XLS export and specific file.

The last check box set if you wish to keep copy of images where the detection spots will be displayed as you set in the following display section. This also displays ROIs. Useful for control. The binary image is a black and white image showing what final part of the image (considering filtering) have been used.

The XLS Output look like the following image. All info about the detection are stored in it: date, input type with file name, pre processor, detector with settings, list of ROI with a summary containing id, ROI name, surface, number of detection, tags. Then a detailed list of detection is displayed with all detection’s centroids (x,y,z,t) and its surface in pixels.

The export to swimming pool option enables the storage of detection in an area where all other plugins can grab the detection. Use this option if you wish to use a particule tracking plugin based on your detections.

XML Output

The XML ouput is perfect for a batch containing a large number of file. You can then drag and drop the XML file into Excel to use the its sorting feature (see image). Warning: if the XML file already exists, information will be appened to it. Select a new one or delete the previous one to avoid this.

Display

 

 

 

 

The last display section let you choose what information should be displayed over the sequence.

If you perform the detection over a 3D stack, the display will show detections centered on the current Z. This can lead to a blinking feeling while visualizing detections. In this case you should use the project all detections of a same stack to display all the detection corresponding to a same t point.

Ref

J.-C. Olivo-Marin “Extraction of spots in biological images using multi scale products” Pattern recognition, vol. 35-9, pp. 1989-1996, 2002. link to publication.

Plugin structure (for developpers)

It is possible to write a specific process as a plugin. The spot detector will recognize it and will integrate it into its menu. See source code and watch how this is already done for the current modules.

Resources needing this

17 reviews on “Spot Detector

  1. Anonymous
    Hi, I have some ideas for your plugin: 1/ Display the binary image over the input image. 2/ Test the detection over the first image of a sequence instead of all the sequence.
  2. berangere
    Hi, it would be great to add a parameter to count also spots that are located under a certain distance from the ROI created from band (to consider not only spots into, but also affixed to the defined ROI)
  3. Hi, very nice plugin -but i was wondering wether it was possible to have a precreated multiple roi or roi grid to allow batch measure -as it work with roi from sequence but when batch analysis is started loose all created roi and the ri from band does not allow to create roi from scratch thanks in advance
  4. Stephane Dallongeville
    Strong spot detection algorithm with load of setting, some of them could probably be simplified (change scale level by object size for example). Nice documentation effort, thanks !
  5. IcyLyd
    Really great detection. The batch analysis is also very usefull. I would put 5 stars if we could combine "scale 1 union scale 2" and not only "scale1 intersecting scale2".
  6. Alexandre Dufour
    One of Icy's best plug-in just got better... almost there: 5 stars if you adjust wavelet size in Z using the X/Z resolution ratio
  7. Even better after the recent updates!
  8. Hi, great tool to count the spots!! however, when I want to export the data from the ROI window in order to get the areas in um² (because in the xls file saved, the surface is different in an undefined unit), it wont respond and it will block my computer.. thanks for the job!
  9. A very handy plugin when properly configured !
  10. Anonymous
    Very nice tool for beekeepers too! Use to count the number of mites that fall - www.beespace.me
  11. First tests on noisy images are encouraging. Would it be possible to combine two types of filtering (area and diameter)? And to add the possibility of a manual curating (adding missed objects, and removing false positives) ?
  12. INSERM
    An extremely useful and very accurate plugin. A plus would be an option to filter the spots according to their integrated or maximal intensity.

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Changelog

  • Version 1.7.0.0 • Released on: 2018-12-20 11:46:28
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    Description:

    Now considers t and z of ROIs in filtering

  • Version 1.6.0.4 • Released on: 2018-12-19 14:36:22
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    Description:

    minor fix

  • Version 1.6.0.3 • Released on: 2018-12-19 14:18:02
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    Description:

    fix the black area for ROI2DArea

  • Version 1.6.0.2 • Released on: 2016-10-24 14:44:31
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    Description:

    batch file import fixed with new kernel version

  • Version 1.6.0.1 • Released on: 2016-02-10 13:29:44
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    Description:

    New GUI
    New default export

  • Version 1.6.0.0 • Released on: 2015-05-05 17:24:36
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    Description:

    You can now specify a new detector from an third party plugin

  • Version 1.5.0.8 • Released on: 2015-02-12 18:22:23
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    Description:

    Fix: The append to xls file is re-working

  • Version 1.5.0.7 • Released on: 2014-12-04 15:21:10
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    Description:

    Minor fix for test purposes

  • Version 1.5.0.6 • Released on: 2014-06-10 18:02:31
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    Description:

    Little Change in vtkRendering

  • Version 1.5.0.5 • Released on: 2014-05-19 18:16:25
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    Description:

    Minor fix to comply with new VTK lib.

  • Version 1.5.0.4 • Released on: 2014-04-25 14:10:32
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    Description:

    XLS export is now using XLSUtil instead of XLSManager

  • Version 1.5.0.3 • Released on: 2014-04-24 17:33:30
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    Description:

    Added: some code to obtain more explicit bug reports

  • Version 1.5.0.2 • Released on: 2014-04-07 12:03:46
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    Description:

    Fix the ROI export in 3D: some ROIs were not properly set in Z.

  • Version 1.5.0.1 • Released on: 2014-03-13 16:45:53
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    Description:

    minor fix: renaming bands to channels

  • Version 1.5.0.0 • Released on: 2014-03-07 18:21:54
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    Description:

    - Now exports spots as ROIs (named spot #number)
    - Threshold in wavelet detector is now named sensitivity
    - The approximative size of the objects detected by each scale is now displayed
    - The binary stack output are now saved in 1 file instead of multiple files
    - The filtering (range of size in pixel) is now fixed
    - The interval graphical component is removed
    - Force 2D wavelets for 3D is now functional

  • Version 1.4.1.9 • Released on: 2013-12-05 13:11:11
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    Description:

    Minor fix

  • Version 1.4.1.8 • Released on: 2013-12-04 11:15:34
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    Description:

    Improved: If the sequence has no file name, the swimming pool output takes its name as a label.

  • Version 1.4.1.7 • Released on: 2013-12-03 14:58:59
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    Description:

    max size for spot filtering is now 3000 instead of 300

  • Version 1.4.1.6 • Released on: 2013-07-12 15:58:18
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    Description:

    - Added: display: option to display detection index (not displayed by default)

  • Version 1.4.1.5 • Released on: 2013-06-15 16:04:05
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    Description:

    - Automatic creation of ROI now creates named roi with AREA# to find them easialy in the excel output file.

  • Version 1.4.1.4 • Released on: 2013-04-23 15:41:22
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    Description:

    Added the support of ROIs for scripts using the object UDWTWavelet

  • Version 1.4.1.3 • Released on: 2013-02-05 17:34:36
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    Description:

    add a class to call the wavelet in an easy manner from scripts

  • Version 1.4.1.2 • Released on: 2013-01-28 10:29:00
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    Description:

    Minor change

  • Version 1.4.1.1 • Released on: 2012-11-13 15:28:05
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    Description:

    The automatic generation of ROI can now dilate found ROIs

  • Version 1.4.1.0 • Released on: 2012-10-15 13:53:56
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    Description:

    - Memory consumption reduced

  • Version 1.4.0.7 • Released on: 2012-08-23 17:32:38
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    Description:

    - fix: The WAT value could be false if no ROI was present in the sequence and the WAT with ROIs enabled.

    - minor changes to fit integration in protocols.

  • Version 1.4.0.6 • Released on: 2012-06-15 16:13:37
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    Description:

    New XML Features:
    -Export tags (in a way Excel can manage it)
    -Export date time of image processing.

    New ROI/Batch feature:
    -New ROIFromFixedSequence: for a batch, you can now set a set of ROI from an active sequence and then apply those ROI(s) to all the batch.

  • Version 1.4.0.5 • Released on: 2012-06-14 18:23:10
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    Description:

    minor bugfix.

  • Version 1.4.0.4 • Released on: 2012-06-14 18:19:33
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    Description:

    - Automatic generation of ROIs now works in batch mode

  • Version 1.4.0.3 • Released on: 2012-06-14 17:54:12
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    Description:

    New preProcessor: mean of channel in images.

  • Version 1.4.0.2 • Released on: 2012-06-04 15:47:05
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    Description:

    improved: faster save of binary image

  • Version 1.4.0.1 • Released on: 2012-05-11 10:15:34
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    Description:

    -XML output fields added: file name and folder
    -fix minor error if no sequence is selected as input
    -debug output log removed

  • Version 1.4.0.0 • Released on: 2012-05-10 14:56:08
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    Description:

    New: XML export. See doc for details.

  • Version 1.3.0.1 • Released on: 2011-12-07 16:06:18
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    Description:

    update to fit with new detection data structure

  • Version 1.3.0.0 • Released on: 2011-11-23 17:12:19
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    Description:

    New feature:

    You can now use the *create roi from band* functionality to automaticaly create a mask of all the cells, and then perform a spot count per segmented cell.

  • Version 1.2.0.4 • Released on: 2011-11-14 10:07:40
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    Description:

    Add: Externalisation of the wavelets for external use by other plugins

  • Version 1.2.0.3 • Released on: 2011-10-27 09:54:33
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  • Version 1.2.0.2 • Released on: 2011-10-20 10:21:18
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    Description:

    Batch improvements (to be continued)

  • Version 1.2.0.1 • Released on: 2011-10-06 14:42:31
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    Description:

    stable version

  • Version 1.2.0.0b • Released on: 2011-10-06 13:39:24
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    Description:

    - now computes min,max and average intensity.
    - code cleanup

  • Version 1.1.0.6 • Released on: 2011-09-14 14:25:31
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    Description:

    minor change

  • Version 1.1.0.5 • Released on: 2011-09-14 14:18:46
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    Description:

    Fix: Images are now saved at the correct size.

  • Version 1.1.0.4 • Released on: 2011-09-13 11:40:19
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    Description:

    Fix export

  • Version 1.1.0.3 • Released on: 2011-09-13 11:38:42
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    Description:

    Regression from version 1.1.0.1

  • Version 1.1.0.2 • Released on: 2011-09-13 11:37:26
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    Description:

    Add: link to online documentation.

  • Version 1.1.0.1 • Released on: 2011-08-29 15:22:12
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    Description:

    improved detection GUI

  • Version 1.1.0.0 • Released on: 2011-08-29 13:16:38
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    Description:

    Fix: memory leak.
    Fix: painter are not anymore shared between sequences
    Fix: binary output has no more strange colors
    Fix: an error occured if 2 same batch were launch in a row

  • Version 1.0.2.11 • Released on: 2011-08-17 11:48:50
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  • Version 1.0.2.10 • Released on: 2011-06-16 18:07:59
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    Description:

    Add x y z t in the xls output

  • Version 1.0.2.9 • Released on: 2011-05-03 15:51:59
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    Description:

    Compatibility with last kernel version 1.0.0.5

  • Version 1.0.2.8 • Released on: 2011-04-20 09:52:22
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    Description:

    Fix some issues due to changes in dependency ConnectedComponents

  • Version 1.0.2.7 • Released on: 2011-03-25 17:21:04
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    Description:

    stable release

  • Version 1.0.2.6b • Released on: 2011-03-25 17:17:36
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    Description:

    FIX: when the plugin is closed, the detection represented on the sequence are removed too.

  • Version 1.0.2.5b • Released on: 2011-03-25 16:46:08
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    Description:

    Added: Now exports detections to the swimming pool to communicate with the spot tracker.

  • Version 1.0.2.4 • Released on: 2011-03-15 14:25:24
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    Description:

    Added: Name of ROI displayed over sequence

  • Version 1.0.2.3 • Released on: 2011-03-07 10:11:12
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    Description:

    Added : support tags generated by the plugin ROI Tagger

  • Version 1.0.2.2b • Released on: 2011-03-07 09:58:59
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  • Version 1.0.2.1 • Released on: 2011-02-24 16:38:31
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    Description:

    Added the wavelet adaptive threshold.

  • Version 1.0.2.0 • Released on: 2011-02-16 18:31:53
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    Description:

    Batch input added

  • Version 1.0.1.3 • Released on: 2011-02-16 13:55:15
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    Description:

    removed webcam feature as it is not yet fully stable.

  • Version 1.0.1.2 • Released on: 2011-02-16 13:38:19
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  • Version 1.0.1.1 • Released on: 2011-02-16 13:24:49
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    Description:

    Webcam detection fixed
    Output fixed

  • Version 1.0.1.0 • Released on: 2011-02-10 14:35:12
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    Description:

    Automatic creation of ROI added. This takes on channel and threshold it to drive the detection in an other channel.

  • Version 1.0.0.3 • Released on: 2011-02-09 15:59:45
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  • Version 1.0.0.2 • Released on: 2011-02-09 15:54:15
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  • Version 1.0.0.1 • Released on: 2011-02-09 15:50:50
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  • Version 1.0.0.0 • Released on: 2011-02-09 14:59:24
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