Short Description

This plugin allows one to use various basic sequence operations within Blocks.

Team: Bio Image Analysis
Institution: Institut Pasteur
Website: https://icy.bioimageanalysis.org/
Source code: https://gitlab.pasteur.fr/bia/sequence-blocks

Documentation

This plugin contains the following Blocks :

  • Conversion:
    • Convert Stack: Convert all slices to time or vice-versa
    • Convert Type: Convert the type of the sequence to another type
  • Creation:
    • Create Sequence: create a sequence from nothing or from an image
    • Duplicate Sequence: duplicate input sequence
    • Combine Channels: combine two channels from two sequence (possibly the same). For more than 2 channels, you will have to use more “Combine Channels” blocks
  • Extraction:
    • Extract Channel: extract a channel from the sequence as a new sequence
    • Extract Multi Channels: extract one or more channels from the sequence, as a new sequence. To extract multiple channels, please use spaced numbers or an Array Input of numbers
    • Extract Stack: extract a whole stack at a specified time position
    • Extract Time: extract the whole time for a specified stack position
    • Crop Sequence: crop a new sequence from the input sequence. The area of the crop is defined by a ROI
  • Images:
    • Add Image: add the image into the sequence in the last T position after the last Z
    • Remove Image: remove an image at the specified Z and T position
    • Get Image: get an image from the input sequence at the specified Z and T position
    • Set Image: set an input image in the input sequence at the specified Z and T position
    • As Image Array: the output is an Array of Images, containing all images in the sequence.
  • Infos:
    • Get Metadata: uses a sequence as input, and output all metadata, such as Sequence Name and resolution (1)
    • Set Name: changes the name of the sequence
    • Set Resolution: changes the resolution of the ratio: pixel per millimeter, on X / Y / Z axes.
    • Dimensions: get all the dimensions of the input sequence: width / height / nb channels / nb stacks / nb time positions
    • Property: custom user property
  • Files:
    • Load Sequence: load a sequence from the specified file
    • Save Sequence: saves the input sequence onto the disk at the specified location
    • Is File Valid: tests if the given file has a good extension
  • ROIs:
    • AddRois: Adds one or multiple ROIs to a given sequence.
(1) Pixel Size represents the size of a pixel in millimeters.

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3 reviews on “Sequence Blocks”

  1. Anonymous
    very useful, should be installed by default with protocol
  2. J
    Hi. I tried to use this to concatinate two sequences together, but this block is missing. It would be great to have this function available.
  3. A
    Hello I tried to use the convert stack block but it seems to be missing. It would be great to have it. Thanks

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Changelog

  • Version 2.1.0.0 • Released on: 2021-04-22 11:30:00
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    Description:

    Added new get/set Property blocks

  • Version 2.1.0.0 • Released on: 2020-09-14 17:40:00
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    Description:

    Fixed several issues from Loop blocks

  • Version 2.0.15.0 • Released on: 2020-08-11 16:21:00
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    Description:

    Fixed Sequence region batch null pointer exception bug on declare input.
    Now exposing current ROI as a loop variable

  • Version 2.0.14.0 • Released on: 2020-07-02 18:30:00
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    Description:

    Fixed SequenceFileImporter Loop blocks (need to be very careful about field initialization !!)

  • Version 2.0.13.0 • Released on: 2020-07-02 16:00:00
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    Description:

    Added 'series' field for SequenceFileImporter / Loop blocks + minors fixes (Stephane)

  • Version 2.0.12.0 • Released on: 2020-06-23 15:00:00
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    Description:

    Updated documentation on AddROI block

  • Version 2.0.11.0 • Released on: 2020-06-03 15:05:00
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    Description:

    Fix: Get file name without extension does not remove extension

  • Version 2.0.10.0 • Released on: 2019-08-22 18:00:00
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    Description:

    Added EzVarColormap variable for easy integration in EzPlug plugins.

  • Version 2.0.9.0 • Released on: 2019-06-28 17:00:00
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    Description:

    Fixed a bug with "Set ColorMap" block which can corrupt default colormap

  • Version 2.0.8.0 • Released on: 2019-03-19 13:00:07
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    Description:

    updated "Crop Sequence" block so it accepts both single ROI or array of ROI.

  • Version 2.0.7.0 • Released on: 2019-02-20 12:10:44
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    Description:

    Added a new "Additive Fill Sequence" block to easily build heatmap image from a list of ROIs

  • Version 2.0.6.0 • Released on: 2018-11-19 18:23:02
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    Description:

    Updated for new kernel version (was using internal kernel method).

  • Version 2.0.5.0 • Released on: 2018-10-10 17:17:50
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    Description:

    Fixed loading / saving of Colormap parameter.

  • Version 2.0.4.0 • Released on: 2018-09-12 10:46:05
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    Description:

    Fixed the file format for "Save Sequence" Block.

  • Version 2.0.3.0 • Released on: 2018-06-21 16:28:02
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    Description:

    added "Create Linear Colormap" block to create an arbitrary RGB color colormap

  • Version 2.0.2.0 • Released on: 2017-08-10 17:15:08
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    Description:

    Improved "Save Sequence" block.

  • Version 2.0.1.0 • Released on: 2017-07-06 18:09:31
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    Description:

    minors fixes and tweaks

  • Version 2.0.0.0 • Released on: 2017-06-06 17:14:10
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    Description:

    * new batch blocks:
    - sequence region (ROIs) batch.
    - sequence slice batch.
    - sequence frame batch.
    - sequence channel batch.
    * new SequenceFileImporter blocks:
    - Select Sequence File Importer
    - Sequence File Importer Accept
    - Sequence File Importer Open
    - Sequence File Importer OpenSeries
    - Sequence File Importer Close
    - Sequence File Importer GetMetadata
    - Sequence File Importer GetTileSize
    - Sequence File Importer GetImage
    - Sequence File Importer GetThumbnail
    - Sequence File Importer LoadSequence
    * new SequenceFileImporter batch blocks:
    - Sequence File Importer Series batch
    - Sequence File Importer Tile batch
    - Sequence File Importer Region batch
    - Sequence File Importer Slice batch
    - Sequence File Importer Frame batch
    - Sequence File Importer Channel batch
    * added LoadSubSequence block to load only a sub part of a Sequence.

  • Version 1.8.8.0 • Released on: 2016-04-19 13:36:27
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    Description:

    added 'remove previous' field on "add rois" block

  • Version 1.8.7.0 • Released on: 2016-02-10 12:44:14
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    Description:

    Added 'Get Data Type' block to retrieve the Sequence Data Type.

  • Version 1.8.6.1 • Released on: 2015-10-09 14:39:45
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    Description:

    Some tweaks in file identification.

  • Version 1.8.6.0 • Released on: 2015-10-01 15:56:12
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    Description:

    * added the following blocks:
    - "Add Overlays" / "Remove Overlays"
    - "Add Rois" / "Remove Rois" / "Remove All Rois"
    - "Save Metadata"
    * some minors fixes and tweaks

  • Version 1.8.5.0 • Released on: 2015-07-02 10:55:31
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    Description:

    Added Get/Set Colormap blocks to retrieve / set a specific colormap LUT on image channel.

  • Version 1.8.4.0 • Released on: 2015-02-19 13:26:56
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    Description:

    fixed block ids

  • Version 1.8.3.1 • Released on: 2015-02-19 12:07:17
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    Description:

    Regression from version 1.8.2.0

  • Version 1.8.3.0 • Released on: 2015-02-11 17:45:49
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    Description:

    Cleanup & updated to last Block version.

  • Version 1.8.2.1 • Released on: 2015-01-08 18:58:59
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    Description:

    updated for kernel refactoring

  • Version 1.8.2.0 • Released on: 2014-12-03 18:30:45
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    Description:

    Added 2 new blocks:
    - fill inner Sequence:
    fill the interior of the input ROI with specified value
    - fill outer Sequence:
    fill the exterior of the input ROI with specified value

  • Version 1.8.1.1 • Released on: 2014-12-03 15:01:10
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    Description:

    Changed fill sequence block name.

  • Version 1.8.1.0 • Released on: 2014-12-03 14:59:24
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    Description:

    Added fill sequence block.

  • Version 1.8.0.3 • Released on: 2014-06-03 17:59:58
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    Description:

    Fixed a minor issue with "Save Sequence" block.

  • Version 1.8.0.2 • Released on: 2014-06-03 11:48:25
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    Description:

    Fixed "CropCZT" bloc.

  • Version 1.8.0.1 • Released on: 2014-05-12 17:26:01
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    Description:

    fixed getMetaData params id.

  • Version 1.8.0.0 • Released on: 2014-05-12 16:17:49
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    Description:

    * added new blocs for metadata load / read operations.
    * removed resizeNew bloc and improved original resize bloc instead.
    * others minors changes / tweaks.

  • Version 1.7.2.2 • Released on: 2014-04-28 11:50:26
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    Description:

    typo

  • Version 1.7.2.1 • Released on: 2014-04-28 11:48:04
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    Description:

    Added serie input field for the "load sequence" bloc.

  • Version 1.7.2.0 • Released on: 2014-03-27 13:20:00
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    Description:

    * added 'Convert Color' bloc
    * added 'Resize New' bloc
    * some minors fixes / tweaks

  • Version 1.7.1.0 • Released on: 2013-08-23 18:18:19
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    Description:

    * corrected Resize for backward compatibility

  • Version 1.7.0.0 • Released on: 2013-07-22 15:40:40
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    Description:

    * added Get Name
    * added Get Channel Name
    * added Set channel name
    * added Get resolution (same as Get meta data, name is better and more accurate)

  • Version 1.6.1.0 • Released on: 2013-07-03 14:51:22
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    Description:

    * corrected issues with VarListeners in the Resize block.

  • Version 1.6.0.0 • Released on: 2013-07-03 11:18:19
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    Description:

    * added a Resize block.

  • Version 1.5.0.0 • Released on: 2013-06-05 14:16:44
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    Description:

    * Corrected bug in Combine Channels.

  • Version 1.4.0.0 • Released on: 2013-05-22 15:39:42
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    Description:

    * Corrected issue with Save Sequence

  • Version 1.3.2.1b • Released on: 2013-03-13 16:51:26
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    Description:

    Corrected error about extractStack not found.

  • Version 1.3.2.0 • Released on: 2013-03-12 13:31:47
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    Description:

    Now appears under the "Sequence" section in Protocols!

  • Version 1.2.1.4 • Released on: 2013-02-28 17:11:04
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    Description:

    Fixed set pixel resolution bloc.

  • Version 1.2.1.3 • Released on: 2013-02-28 17:08:39
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    Description:

    Regression from version 1.2.0.0

  • Version 1.2.1.2 • Released on: 2013-02-28 16:59:36
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    Description:

    Regression from version 1.2.0.0

  • Version 1.2.1.1 • Released on: 2013-02-28 16:57:50
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    Description:

    Fixed set pixel resolution bloc.

  • Version 1.2.0.0 • Released on: 2013-01-07 16:30:00
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    Description:

    Corrected an inversion between Extract Time and Extract Slice

  • Version 1.1.0.1 • Released on: 2012-10-22 14:12:41
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    Description:

    * corrected issue with file blocks

  • Version 1.1.0.0 • Released on: 2012-10-17 13:58:03
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    Description:

    * Block with File inputs are now mutable, they can have a string as a parameter

  • Version 1.0.2.0 • Released on: 2012-09-27 11:22:17
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    Description:

    Added an option in SaveSequence block to save in multiple file.

  • Version 1.0.1.0 • Released on: 2012-09-06 10:43:32
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    Description:

    Added sequence getFilename() block to retrieve the filename used to open / save a sequence.

  • Version 1.0.0.2 • Released on: 2012-08-22 10:33:26
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    Description:

    Fixed GetMetadata block.

  • Version 1.0.0.1 • Released on: 2012-06-22 15:17:27
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    Description:

    Added Description to the Blocks.
    Corrected Save Sequence block name.

  • Version 1.0.0.0 • Released on: 2012-06-21 15:37:19
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    Description:

    First real version.

  • Version 0.0.1.0 • Released on: 2012-06-21 15:00:05
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