Short Description

Align multidimensional images in 2D or 3D, rigidly or with warping, whatever the difference in scale. Provide also a set of tools for Correlative Light Electron Microscopy, but can be used for registration/alignement of any correlative imaging.

Documentation

Perrine Paul-Gilloteaux and Xavier Heiligenstein

Contact us for any questions, or post in the Icy forum.

This plugin allows to compute a similarity (translation/rotation/scaling and flipping) transform from pair of points. It is updating the transformed image interactively such that the user get immediate feedback. The transformation is saved and can be applied to any other stack/image. Non rigid deformation can also be applied in 2D or 3D.

 

Please make sure to use the last version of the plugin ( update plugins in icy)

3D/3D,2D/3D or 3D /2D can be handled . 3D ROI are enabled, and can be checked with the 3D vtk view (size of ROI can be changed using the ROI stroke width). Some prelalignment by rotating in 3D the volume is possible.
Transformations can be applied directly or combined through Block Protocols (search for apply transformation).
It’s also provide information about the predicted Error (based on statistical prediction as described by Fitzpatrick et al), either as a full color mapping, either on each points used as landmarks, and error on the discrepancy in position between points.

In addition to the video and pdf tutorials, some further information are available here. You may also want to have a look to AUTOFINDER

Authored by Perrine Paul-Gilloteaux and Xavier Heiligenstein.

List of video tutorials:

Introduction to Icy for Ec-Clem (new users of ICY )

Registration in 2D, rigid or non rigid

Registration of a slice to a volume (2D to 3D) (same principle for 3D to 2D, just inverse source and target)

Registration in 3D

Pre registration by 3D volume rotation from 3D viewer.

Reapply a previously computed transform (tutorial in 2D, but exact same procedure for 3D)

Monitoring accuracy

Integrated preprocessing (such as flatening options or denoising)

Register using LINES rather than points (actually using AUTOFINDER)

List of pdf tutorials:

2D-2D step by step PDF

3D-3D step by step PDF

Preprocessing step by step PDF

Register a reconstructed tomogram to 2D fluo in 2D and then merge in 3D

HOW TO CITE US?
Thanks for using eC-CLEM, if you plan to publish your work and made efficient use of this plugin or of the AutoFinder, please cite our publication.

 

 

Introduction to Icy for new Icy users:

First step for manual 2D-2D rigid registration:

Computing a non linear transformation:

2D to 3D rigid registration in EC-CLEM:

3D to 3D rigid registration:

Pre processing options:

Monitoring a target point accuracy:

Applying a previously computed transform:

Prealign in 3D (3D rotate/flipping in any direction):

Align line even if not perfectly matching :

Select Options, Source (image/volume to be transformed)and Target (referece image), Note that you do not need to crop, rescale or change the size of your datasets to use EC-CLEM.

Press Play to initialize placement of points.

For 2D: place points on target image, on image source drag it on the correct position. After 3 points, images will be automatically updated when added a new point. Transfirmations are saved in a file named after the source file suffixed transfo.xml

For 3D: Same principle: it is advised to use the duplicate view capacity of ICY to follow the pacement of points in 3D. For now, make sure to go to the slice of source image containing the landmarks you will add in target image. After 4 points, stacks will be automatically updated.

For both 2 D and 3D, if you select the let me update myself option: the transformation will be computed only once you pressed Update Transformation. You can add more points and click again “Update the transformation” to update the transformation.

The non rigid option work also based on landmarks, in 2D or in 3D directlly. Note that the image will be warped such that the landmark are now in the same position. Press

In want to prealign (rotate in 3D)” will allow that you turn the 3D view (VTK Canvas) and then generate a transformation saved as xml as well and a new stack in the interactively indiacted view (useful to flip a 3D volume for example).

Apply transformation can also be apply in a protocol (in you combined a 3D prealignement (_MANUAL TRANSFO.xml), with a 3D RIGID transformation, followed by a NON RIGID deformation,) , you can create an Icy protocol to cascade these transformations with the Apply Transformation block.

 

  • 2D option: will compute a transform ignoring the Z position of the landmarkes points, but it can be applied to multidimensional dataset.
  • 3D option: can be used to compute 3D to 3D, 2D to 3D (placing a reoriented slice in a 3D volume), 3D to 2D (extracting a reoriented 2D slice from a volume)
  • Non rigid: use with caution at it will warp your image (an infinity of solutions are possible here…) It is advsed that you use a rigid transform first: EC CLEM will advise you to go or not to a non rigid deformation, based upon the difference between an expected error after rigid registration, and the actual error observed on used landmarks.

 

 

 

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Changelog

  • Version 1.0.1.5 • Released on: 2018-10-06 12:04:21
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    Description:

    WARNING! for now bug in ICY core 1.9.9 for the 3D visualization, lease stick to Icy 1.9.8 while this bug is fiexed by the ICY team.

    - New version of ec-clem:
    - Update the error validation plugin to be compatible with Icy >1.9
    - Add a few back up of the transformation and roi points, saved as xml to stop and restrat a manual transformation.
    - Fixed a bug on The roi format for old ROI.

  • Version 1.0.1.4 • Released on: 2018-07-24 15:57:29
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    Description:

    fixed th bug from 1.0.1.2

  • Version 1.0.1.3 • Released on: 2018-07-24 15:13:50
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    Description:

    Regression from version 1.0.1.1

  • Version 1.0.1.2 • Released on: 2018-07-24 10:26:38
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    Description:

    update for better range conservation.
    * tested with
    * Unsigned bit (8 bit) : no loss
    * signed bit (7 bit + one signed bit): some slight loss
    * unsigned short (16 bit): no loss
    * signed short (15 bit plus 1 bit sign): no loss
    * unsigned int: some slight loss
    * signed int some slight loss
    * float some slight loss
    * double :some slight loss

    For lossy conversion, rather use ApplytransformationtoROI if you need an accurate measurement.
    (Available from advancedOption or by direct search)

  • Version 1.0.1.1 • Released on: 2018-02-19 18:00:16
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    Description:

    Add a ApplyTransformationtoRoi plugin, available from the search bar only or in the protocol blocks list only for now.
    This plugin apply the transformation contained in *-transfo.xml to the ROI (such as an area to be measured) and display the transformed ROI on the target image.

  • Version 1.0.1.0 • Released on: 2017-10-10 09:32:21
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    Description:

    - ensure retrocompatibility with old ROI from ec-clem
    - catch more possible errors

  • Version 1.0.0.9 • Released on: 2017-10-09 13:10:07
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    Description:

    - add an option to import csv file separated by comma and semi comma
    - do not erase ROI anymore when the number of ROI is different, but points named Point2D or Point3D (due to clicking on source rather than target image when placing points)
    - add a back up of ROIs when clicking on Clear all landmarks (check the console to know the filename): they can be loaded back from ICY.

  • Version 1.0.0.8 • Released on: 2017-08-23 18:48:35
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    Description:

    - Important: Correct Apply Scaled Transfo in 3D and 2D
    - some code cleaning
    - add a warning if the xml doc is not accessible anymore (usb stick etc..)
    (ec-clem is on GitHub)

  • Version 1.0.0.7 • Released on: 2017-08-18 11:20:44
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    Description:

    - importRoiPointsFromFile : Add an option to have x,y in physical units,
    with an offset of 1 (slice 1 is 0 in Icy) + modify the type of ROI to
    ROI 3D point + add the name to easily see the center of gravity of the
    3D point.

    - ec-clem : fixed a bug on "show Roi on source image" by adding the
    correct pixel size in 3D. The bug was only hapening when the pixel size
    were different in source and target image.

    - minor ecclem: change the type conversion after 2D transform
    (deprecated method in icy)
    -minor ec-clem : remove an unused variable+ update sequence
    concatenation according to icy api last updates.

  • Version 1.0.0.6 • Released on: 2017-06-16 17:43:09
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    Description:

    - adapt the code to 1.9.2 (fixing the bug report when pressing the stop button + Deprecated methods updated).

  • Version 1.0.0.5 • Released on: 2017-05-31 21:44:40
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    Description:

    - fix a few bugs (transformed saved image could not be saved, this is fixed + Some error regarding xml file reading taht should be fixed (could not reproduce..) . Please send any detail on the context and the console content when reporting this bug

  • Version 1.0.0.4 • Released on: 2017-04-11 12:42:51
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    Description:

    - remove extra message in the console

  • Version 1.0.0.3 • Released on: 2017-04-11 12:22:29
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    Description:

    - Now use draggable 3D ROI
    - Message can be removed (do not show again)
    - Now you need to RIGHT CLICK for validate a point after dragging on source image

  • Version 1.0.0.2 • Released on: 2017-04-11 12:21:27
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    Description:

    Regression from version 1.0.0.0

  • Version 1.0.0.1 • Released on: 2017-04-11 12:20:20
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    Description:

    - Now use draggable 3D ROI
    - Message can be removed (do not show again)
    - Now you need to RIGHT CLICK for validate a point after dragging on source image

  • Version 1.0.0.0 • Released on: 2017-03-24 18:42:20
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    Description:

    -- fixed some bugs (related to filenames created by autofinder)

    -- add the display of the TOTAL transform when pressing Stop (for similiarity only, 2D and 3D)

    - ImportRoiPointsFromFile and ConvertBinarytoPointRoi are now callable
    from protocols (blocks) to construct advanced registration workflow

    -Preprocess3Dstackto2D: make it robust to change of active sequence during processing

  • Version 0.2.1.2 • Released on: 2016-12-13 13:41:38
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    Description:

    Applytransformation: set also the output sequence for block protocol (was not set and was returning the same image when the transformation came from AUTOFINDER)

  • Version 0.2.1.1 • Released on: 2016-11-30 05:15:31
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    Description:

    -apply transform can now read the autofinder output transform
    - pixel size was not updated when applying a 2D transformation computed fro ec-clem, fixed

  • Version 0.2.1.0 • Released on: 2016-11-08 11:52:09
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    Description:

    - add the automatic reading of the current version and put it first line

  • Version 0.2.0.11 • Released on: 2016-10-16 22:40:34
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    Description:

    - progress bar also for non rigid and 3D let me update (was not running as background task)
    - Keep the LUT setting in 2D or 3D on the fly settings (remove autobound)

  • Version 0.2.0.10 • Released on: 2016-10-11 16:27:47
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    Description:

    - Preprocessing: Add a warning or set up instruction if EPFL plugin is not installed
    - Fix a small bug on non rigid registration (viewer related)

  • Version 0.2.0.9 • Released on: 2016-10-01 18:03:19
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    Description:

    - fixed few bugs

  • Version 0.2.0.8 • Released on: 2016-08-08 12:21:49
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    Description:

    - Modify the apply scaled transfo to get the full view of the transformed image
    - Change the conditions of error analysis
    - Stop the listeners to ROI when stopping ec-clem
    - Remove the limitation on different size for non rigid transformation

  • Version 0.2.0.7 • Released on: 2016-08-04 17:15:56
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    Description:

    fixed the wavy "warning" bug

  • Version 0.2.0.6 • Released on: 2016-08-04 15:19:26
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    Description:

    non beta

  • Version 0.2.0.5b • Released on: 2016-08-04 14:32:22
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    Description:

    -bad class name for autofinder

  • Version 0.2.0.4b • Released on: 2016-08-04 14:15:56
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    Description:

    Added more messages
    Added error study
    Correct a few bugs

  • Version 0.2.0.3 • Released on: 2016-07-29 17:25:07
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    Description:

    -change the roi definition such that in 3D, point as a new zd value (dispalyed in 3D) in additionn to z value (displayed on 2D slice) so that the 3D transform is more accurate when updated.
    - schanged the main iterface
    - add a plugin to validate the prediction of error done

  • Version 0.2.0.2 • Released on: 2016-07-21 17:17:07
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    Description:

    - Change the error map representation
    - Fix the 3D basis for Thin Plate Spline Non Rigid deformation
    - ENhance the 2D non rigid grid representation (thicker line), and correct the 3D grid)
    - Add an Advanced Options button.
    - Modify the Apply a scale transfo with binning input rather than pixel size

  • Version 0.2.0.1 • Released on: 2016-07-12 18:32:15
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    Description:

    - change back width line for grid to 1.
    - AutoFinder is still in beta version

  • Version 0.2.0.0 • Released on: 2016-07-12 16:29:22
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    Description:

    - Add an autoFinder plugin (to Find Em area of interest on Lm for example)

  • Version 0.1.0.9 • Released on: 2016-07-08 13:22:31
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    Description:

    - Corect some bug,
    - add the 3D rotation, whatever the file format
    - Add block protocol to apply transformation

  • Version 0.1.0.8 • Released on: 2016-07-07 17:07:01
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    Description:

    - Add the non rigid transformation
    - Add an automatic detection of non rgid transformation needed or not
    - Add the possibility of monitoring a point on source point.
    - Fixed bugs

  • Version 0.1.0.7 • Released on: 2016-05-30 09:31:47
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    Description:

    fixed few bugs when unexpected user behaviour
    Add a monitor target point
    add a 2D and 3D pause mode (let me update myself)

  • Version 0.1.0.6 • Released on: 2016-04-20 12:17:40
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    Description:

    - make it compatible also with java 1.6 for older installation of java. In future version it is advised that you update at least to java 1.7, 1.6 will not be supported anymore

  • Version 0.1.0.5b • Released on: 2016-04-20 00:30:01
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    Description:

    - add the display on roi on original source file (to save roi for example)
    - add a pause mode (by chosing 3D but let le some time, no transfo will be computed unti 'update transfo ' is pressed.

  • Version 0.1.0.4b • Released on: 2016-03-10 16:51:23
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    Description:

    Added the very expected UNDO. You can reverse sevreal times, back to original image like this. The purpose is not to lose any point editio in case of badly placed point.

  • Version 0.1.0.3b • Released on: 2016-02-09 17:37:36
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    Description:

    -add support of RGB images and fixed a bug with unsigned/signed type

  • Version 0.1.0.2b • Released on: 2015-11-09 18:06:36
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    Description:

    - Added the support of multichannel images for the flatten option in preprocessing when calling EPFL plugin EDF.

  • Version 0.1.0.1b • Released on: 2015-11-08 23:47:37
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    Description:

    - made some updates in ensure compatiblity with 1.7.2.0 (made it independnat from loci)+ changes due to ROI updtaes (but still compatible with previous version)

  • Version 0.1.0.0b • Released on: 2015-09-25 18:21:40
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    Description:

    - Fix an error in 2D on TRE computation
    - Modify the display of error as difference in positions from circle to arrow.
    - Fix a bug on the 3D matrix computation
    -Add the version number on the gui interface
    -compiled with java 1.8 but tesing compliance to 1.6 or 1.7

  • Version 0.0.1.20b • Released on: 2015-07-23 11:08:15
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    Description:

    3D/3D and 2D/3D 3D/2D is now enabled

  • Version 0.0.1.19b • Released on: 2015-06-29 03:09:58
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    Description:

    -3D transform correction (to take multichannel coorection into account) + degenerate case is processed: still some pb for the 3D to 2D

  • Version 0.0.1.18b • Released on: 2015-06-29 00:21:58
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    Description:

    Denoising parameters has been optimized based on the size of object of interest. A background substraction step have been added.

  • Version 0.0.1.17b • Released on: 2015-06-14 20:40:00
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    Description:

    - Display problem solved (black images were created)
    - 3D registration is now working as 2D, but not yet totally for 3D to 2D projection

  • Version 0.0.1.16b • Released on: 2015-06-12 17:07:15
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    Description:

    - BUG on 2D transform corrected
    - Preprocessing options added (interface is now simplified to 2D or 3D registration only)

  • Version 0.0.1.15b • Released on: 2015-04-28 15:59:00
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    Description:

    - LUT (pb when conversion from a data type to the same datatype under soime conditions, to discussed with Stephane) : not convert when good type.

  • Version 0.0.1.14b • Released on: 2015-04-24 15:14:30
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    Description:

    3D transform is now available (see doc)
    Warning1: update Transformation is recomputing scale and Anisotropie is not taken into account yet. This will be solved for te first Non Beta Version.

    Warning 2: LUT system has been updated in ICY core: this would have to be ckecked more carefully since it seems to have changed the Scalers as well.

  • Version 0.0.1.13b • Released on: 2015-02-17 09:45:53
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    Description:

    compiled with java jre 1.6

  • Version 0.0.1.12b • Released on: 2015-02-08 17:25:29
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    Description:

    - compiled in java 1.6 (was 1.8 from 1.9)

  • Version 0.0.1.11b • Released on: 2015-02-02 13:45:08
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    Description:

    Fix a bug on the TRE value (was squared)

  • Version 0.0.1.10b • Released on: 2015-01-15 14:09:23
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    Description:

    correct the jar file

  • Version 0.0.1.9b • Released on: 2015-01-14 17:39:33
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    Description:

    - bug fixing
    - Correction of the TRE map and prediction

  • Version 0.0.1.8b • Released on: 2014-11-04 16:16:35
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    Description:

    -LUT colormaps are respected in the overlay

  • Version 0.0.1.7b • Released on: 2014-10-31 17:54:03
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    Description:

    -Robustness add to some unexpected user behaviour (such as button pressed etc...)

  • Version 0.0.1.6b • Released on: 2014-10-30 17:22:00
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    Description:

    - LUT is now respected while adding points
    - interface have been changed.
    - source window will kept the same size as target window after the first transfo.
    - TRE map has now a common color code (green 1000nm, red to yellow between)
    - WARNING: 3D still to be tested (not to be tested in this version).

  • Version 0.0.1.5b • Released on: 2014-10-17 17:31:25
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    Description:

    -correct a bug for overlay at the end when image types were different

  • Version 0.0.1.4b • Released on: 2014-10-17 17:09:11
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    Description:

    - Error Map is now in Float (compatible with Fiji/Icy 32 bits format)
    - An overlay of the two current view is proposed while pressing stop.

  • Version 0.0.1.3b • Released on: 2014-10-16 18:17:35
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    Description:

    Support 3D stack (still 2D registration) , Movie, and Multi Channel for source image to be transformed.
    Error on position circle corrected (were half the size)
    Interface simplified.

  • Version 0.0.1.2b • Released on: 2014-10-01 10:50:55
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    Description:

    none

  • Version 0.0.1.1b • Released on: 2014-10-01 10:40:56
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    Description:

    - flipping taken into account, changes (combined transfo) applied to the original image every time, target can be smaller than source.

  • Version 0.0.1.0b • Released on: 2014-09-10 14:02:27
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