Difference between revisions of "Presentations"

(ImageJ presentations: Use better link for 2010 ImageJDev presentation)
(Add old LOCI ImageJ2 talks, migrated from http://developer.imagej.net/2010/04/07/recent-fiji-imagej2-presentations)
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= ImageJ presentations =
+
{{Learn}}__TOC__
  
{| class="wikitable nicetable" style="width: 100%"
+
== Living workshops ==
| '''Date'''
+
 
| '''Presenter'''
+
These materials are regularly updated, and intended to teach ImageJ and Fiji at introductory, intermediate and advanced levels. The [[LOCI]] group uses them to teach ImageJ at the [http://www.mbl.edu/education/courses/analytical-quantitative-light-microscopy/ AQLM] course every year, as well as locally.
| '''Title'''
+
 
| '''Resources'''
+
{| class="program"
 +
!
 +
! style="padding-left: 10px !important" | '''Title'''
 +
! style="padding-left: 10px !important" | '''Resources'''
 +
|-
 +
| rowspan="3" style="padding: 0 !important" | [[File:fiji-intro-slide.png|300px|link=http://imagej.github.io/presentations/fiji-introduction/]]
 +
| style="font-size: 24px; padding: 0.3em 1em 0.3em 10px !important" | Introduction to Fiji
 +
| style="font-size: 24px; padding: 0.3em 1em 0.3em 10px !important" | [http://imagej.github.io/presentations/fiji-introduction/ slides], [https://vimeo.com/218520761 video]
 +
|-
 +
| style="font-size: 24px; padding: 0.3em 1em 0.3em 10px !important" | Segmentation in Fiji
 +
| style="font-size: 24px; padding: 0.3em 1em 0.3em 10px !important" | [http://imagej.github.io/presentations/fiji-segmentation/ slides], [https://vimeo.com/218520761#t=1h05m49s video]
 +
|-
 +
| style="font-size: 24px; padding: 0.3em 1em 0.3em 10px !important" | Scripting with Fiji
 +
| style="font-size: 24px; padding: 0.3em 1em 0.3em 10px !important" | [http://imagej.github.io/presentations/fiji-scripting/ slides], [https://vimeo.com/218520432 video]
 +
|}
 +
 
 +
== Talks ==
 +
 
 +
{| class="program"
 +
! '''Date'''
 +
! '''Presenter'''
 +
! '''Title'''
 +
! '''Resources'''
 +
|-
 +
| colspan=5 class="section-major" | '''[http://eubias.org/NEUBIAS/neubias2020-conference/symposium2017-lisbon/ 2017 NEUBIAS2020]'''
 +
|-
 +
| 2017-Feb-16
 +
| {{Person|Rueden}}
 +
| What's New in ImageJ2 ?
 +
|
 +
[http://imagej.github.io/presentations/2017-02-16-imagej2-neubias/#/ slides]
 
|-
 
|-
| colspan=5 style="background: lightsteelblue; text-align: center; padding: 0 !important" | '''[[Conference 2015|2015 ImageJ Conference]]'''
+
| colspan=5 class="section-major" | '''[[Conference 2015|2015 ImageJ Conference]]'''
 
|-
 
|-
| colspan=5 style="background: lightgray; text-align: center; padding: 0 !important" | Keynotes
+
| colspan=5 class="section-minor" | Keynotes
 
|-
 
|-
 
| 2015-Sep-03
 
| 2015-Sep-03
| {{Dev | id=rasband}}
+
| {{Person|rasband}}
 
| Introduction to ImageJ
 
| Introduction to ImageJ
 
|
 
|
Line 18: Line 48:
 
|-
 
|-
 
| 2015-Sep-03
 
| 2015-Sep-03
| [[User:Rueden|Curtis Rueden]]
+
| {{Person|Rueden}}
 
| ImageJ2 and Fiji: The ImageJ2 platform, and the Fiji distribution of ImageJ
 
| ImageJ2 and Fiji: The ImageJ2 platform, and the Fiji distribution of ImageJ
 
|
 
|
Line 25: Line 55:
 
|-
 
|-
 
| 2015-Sep-04
 
| 2015-Sep-04
| {{Dev | id=marktsuchida}}
+
| {{Person|marktsuchida}}
 
| Microscope control and image acquisition with Micro-Manager
 
| Microscope control and image acquisition with Micro-Manager
 
|
 
|
Line 31: Line 61:
 
|-
 
|-
 
| 2015-Sep-04
 
| 2015-Sep-04
| {{Dev | id=fjug}}
+
| {{Person|Jug}}
 
| Getting stuff done – Software synergy with ImageJ + KNIME
 
| Getting stuff done – Software synergy with ImageJ + KNIME
 
|
 
|
 
[https://vimeo.com/140098839 video]
 
[https://vimeo.com/140098839 video]
 
|-
 
|-
| colspan=5 style="background: lightgray; text-align: center; padding: 0 !important" | Featured presentations
+
| colspan=5 class="section-minor" | Featured presentations
 
|-
 
|-
 
| 2015-Sep-04
 
| 2015-Sep-04
| {{Dev | id=omsai}}
+
| {{Person|omsai}}
 
| Sharing the value of software freedom with non-programmers
 
| Sharing the value of software freedom with non-programmers
 
|
 
|
 
[https://vimeo.com/140098825 video],
 
[https://vimeo.com/140098825 video],
[http://conference.imagej.net/2015/pariksheet-nanda/transcript.pdf transcript],
+
[[Conference 2015 Program#Pariksheet_Nanda_-_Sharing_the_value_of_software_freedom_with_non-programmers|abstract]],
[[Conference 2015 Program#Pariksheet_Nanda_-_Sharing_the_value_of_software_freedom_with_non-programmers|abstract]]
+
[http://conference.imagej.net/2015/pariksheet-nanda/transcript.pdf transcript]
 
|-
 
|-
 
| 2015-Sep-04
 
| 2015-Sep-04
| [[User:Tiago|Tiago Ferreira]]
+
| {{Person|Tiago}}
 
| Alternative approaches for neuronal morphometry
 
| Alternative approaches for neuronal morphometry
 
|
 
|
Line 54: Line 84:
 
|-
 
|-
 
| 2015-Sep-03
 
| 2015-Sep-03
| {{Dev | id=bogovicj}}
+
| {{Person|Bogovic}}
 
| The Thin Plate Spline method for smooth non-rigid transformations
 
| The Thin Plate Spline method for smooth non-rigid transformations
 
|
 
|
 
[https://vimeo.com/140929688 video],
 
[https://vimeo.com/140929688 video],
[http://conference.imagej.net/2015/john-bogovic/2015_imagej.pptx slides],
+
[[Conference 2015 Program#John_Bogovic_-_The_Thin_Plate_Spline_method_for_smooth_non-rigid_transformations|abstract]],
[[Conference 2015 Program#John_Bogovic_-_The_Thin_Plate_Spline_method_for_smooth_non-rigid_transformations|abstract]]
+
[http://conference.imagej.net/2015/john-bogovic/2015_imagej.pptx slides]
 
|-
 
|-
| colspan=5 style="background: lightgray; text-align: center; padding: 0 !important" | Lightning talks
+
| colspan=5 class="section-minor" | Lightning talks
 +
|-
 +
| 2015-Sep-04
 +
| Anne Alerding
 +
| Quantifying soybean stem tissues using common tools in ImageJ & Fiji
 +
|
 +
[https://vimeo.com/140098824 video],
 +
[[Conference 2015 Program#Anne_Alerding_-_Quantifying_soybean_stem_tissues_using_common_tools_in_ImageJ_.26_Fiji|abstract]]
 
|-
 
|-
 
| 2015-Sep-03
 
| 2015-Sep-03
| [[User:Hinerm|Mark Hiner]]
+
| {{Person|Fab14}}
 +
| Yet another ImageJ friend: Icy
 +
|
 +
[https://vimeo.com/140929690 video],
 +
[[Conference 2015 Program#Fabrice_de_Chaumont_-_Yet_another_ImageJ_friend:_Icy|abstract]]
 +
|-
 +
| 2015-Sep-03
 +
| Jesus Manuel Falagan
 +
| Plugins to import, visualize, process & write astronomical FITS files
 +
|
 +
[https://vimeo.com/140929695 video],
 +
[[Conference 2015 Program#Jesus_Manuel_Falagan_-_Plugins_to_import.2C_visualize.2C_process_.26_write_astronomical_FITS_files|abstract]]
 +
|-
 +
| 2015-Sep-04
 +
| Bill Heeschen
 +
| Quantitative characterization of cellular irregularities in extruded polystyrene foam using digital image processing and analysis
 +
|
 +
[https://vimeo.com/140098843 video],
 +
[[Conference 2015 Program#Bill_Heeschen_-_Quantitative_characterization_of_cellular_irregularities_in_extruded_polystyrene_foam_using_digital_image_processing_and_analysis|abstract]],
 +
[http://conference.imagej.net/2015/bill-heeschen/Heeschen_2015ImageJConf_FoamPatternMacros.ijm macro],<br>
 +
[http://conference.imagej.net/2015/bill-heeschen/Heeschen_2015ImageJConf_TalkSlides.pdf slides (PDF)],
 +
[http://conference.imagej.net/2015/bill-heeschen/Heeschen_2015ImageJConf_TalkSlides.pptx slides (PPTX)]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|Hinerm}}
 
| ImageJ+MATLAB: Reunited
 
| ImageJ+MATLAB: Reunited
 
|
 
|
 
[https://vimeo.com/140929686 video],
 
[https://vimeo.com/140929686 video],
[https://imagej.github.io/presentations/2015-09-03-imagej-matlab/ slides],
+
[[Conference 2015 Program#Mark_Hiner_-_ImageJ.2BMATLAB:_Reunited|abstract]],
[[Conference 2015 Program#Mark_Hiner_-_ImageJ.2BMATLAB:_Reunited|abstract]]
+
[https://imagej.github.io/presentations/2015-09-03-imagej-matlab/ slides]
 +
|-
 +
| 2015-Sep-04
 +
| Irene Landrum
 +
| SWAMP – a no-cost, open, high-performance computing platform for continuous software assurance
 +
|
 +
[https://vimeo.com/140098818 video],
 +
[[Conference 2015 Program#Irene_Landrum_-_SWAMP_.E2.80.93_a_no-cost.2C_open.2C_high-performance_computing_platform_for_continuous_software_assurance|abstract]],
 +
[http://conference.imagej.net/2015/irene-landrum/SWAMP%20%20Presentation%202015Aug25.pptx slides]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|Linkert}}
 +
|  OME Bio-Formats: 10 years of proprietary image data
 +
|
 +
[https://vimeo.com/140929689 video],
 +
[[Conference 2015 Program#Melissa_Linkert_-_OME_Bio-Formats:_10_years_of_proprietary_image_data|abstract]],
 +
[http://ome.github.io/presentations/2015/bioformats-overview-imagej-conf/ slides]
 +
|-
 +
| 2015-Sep-03
 +
| Michael Majurski
 +
| Accurate and scalable Microscopy Image Stitching Tool (MIST)
 +
|
 +
[https://vimeo.com/140929697 video],
 +
[[Conference 2015 Program#Michael_Majurski_-_Accurate_and_scalable_Microscopy_Image_Stitching_Tool_.28MIST.29|abstract]]
 +
|-
 +
| 2015-Sep-04
 +
| {{Person|Bnanes}}
 +
| Slide Set: Simplified batch processing with ImageJ2
 +
|
 +
[https://vimeo.com/140098828 video],
 +
[[Conference 2015 Program#Benjamin_Nanes_-_Slide_Set:_Simplified_batch_processing_with_ImageJ2|abstract]]
 
|-
 
|-
 
| 2015-Sep-04
 
| 2015-Sep-04
| {{Dev | id=bnorthan}}
+
| {{Person|bnorthan}}
 
| Flexible Deconvolution using ImageJ Ops
 
| Flexible Deconvolution using ImageJ Ops
 
|
 
|
 
[https://vimeo.com/140098821 video],
 
[https://vimeo.com/140098821 video],
[https://imagej.github.io/presentations/2015-09-04-imagej2-deconvolution/ slides],
+
[[Conference 2015 Program#Brian_Northan_-_Flexible_deconvolution_using_ImageJ_Ops|abstract]],
[[Conference 2015 Program#Brian_Northan_-_Flexible_deconvolution_using_ImageJ_Ops|abstract]]
+
[https://imagej.github.io/presentations/2015-09-04-imagej2-deconvolution/ slides]
 +
|-
 +
| 2015-Sep-04
 +
| {{Person|Saalfeld}}
 +
| Seamless stitching without blending
 +
|
 +
[https://vimeo.com/140098840 video],
 +
[[Conference 2015 Program#Stephan_Saalfeld_-_Seamless_stitching_without_blending|abstract]]
 +
|-
 +
| 2015-Sep-04
 +
| Raghavender Sahdev
 +
| TimeLapseReg – An ImageJ plugin for drift correction of video sequence in time-lapse microscopy
 +
|
 +
[https://vimeo.com/140098822 video],
 +
[[Conference 2015 Program#Raghavender_Sahdev_-_TimeLapseReg_.E2.80.93_An_ImageJ_plugin_for_drift_correction_of_video_sequence_in_time-lapse_microscopy|abstract]]
 +
|-
 +
| 2015-Sep-04
 +
| {{Person|Bene}}
 +
| Real-time multi-view deconvolution of time-lapse data on the GPU
 +
|
 +
[https://vimeo.com/140098826 video],
 +
[[Conference 2015 Program#Benjamin_Schmid_-_Real-time_multi-view_deconvolution_of_time-lapse_data_on_the_GPU|abstract]]
 +
|-
 +
| 2015-Sep-04
 +
| Amitabh Verma
 +
| Acquisition, processing & re-processing using OpenPolScope plugin for Micro-Manager
 +
|
 +
[https://vimeo.com/140098844 video],
 +
[[Conference 2015 Program#Amitabh_Verma_-_Acquisition.2C_processing_.26_re-processing_using_OpenPolScope_plugin_for_Micro-Manager|abstract]]
 +
|-
 +
| 2015-Sep-04
 +
| {{Person|Twagner}}
 +
|  NanoTrackJ – An open-source multi-modal size characterization tool for nanoparticle tracking analysis based on ImageJ
 +
|
 +
[https://vimeo.com/140098848 video],
 +
[[Conference 2015 Program#Thorsten_Wagner_-_NanoTrackJ_.E2.80.93_An_open-source_multi-modal_size_characterization_tool_for_nanoparticle_tracking_analysis_based_on_ImageJ|abstract]],
 +
[https://dl.dropboxusercontent.com/u/560426/imagej/conference2015/slides.pdf slides]
 +
|-
 +
| 2015-Sep-04
 +
| Petr Walczysko
 +
| The Open Microscopy Environment (OME)
 +
|
 +
[https://vimeo.com/140098837 video],
 +
[[Conference 2015 Program#Petr_Walczysko_-_The_Open_Microscopy_Environment_.28OME.29|abstract]]
 +
|-
 +
| 2015-Sep-04
 +
| {{Person|jaywarrick}}
 +
| JEX – a platform for data management and batch processing with standard tools
 +
|
 +
[https://vimeo.com/140098819 video],
 +
[[Conference 2015 Program#Jay_Warrick_-_JEX_.E2.80.93_a_platform_for_data_management_and_batch_processing_with_standard_tools|abstract]]
 +
|-
 +
| 2015-Sep-03
 +
| Aryeh Weiss
 +
| Automated processing of telomeres with ImageJ and R
 +
|
 +
[https://vimeo.com/140929694 video],
 +
[[Conference 2015 Program#Aryeh_Weiss_-_Automated_processing_of_telomeres_with_ImageJ_and_R|abstract]],
 +
[http://conference.imagej.net/2015/aryeh-weiss/ij2015telomere-A.ppt slides]
 +
|-
 +
| colspan=5 class="section-major" | '''[[Conference 2012|2012 ImageJ Conference]]'''
 +
|-
 +
| 2012-Oct-24
 +
| {{Person|Rueden}}
 +
| ImageJ2: Current Status and Future Directions
 +
|
 +
[http://conference.imagej.net/2012/curtis-rueden/2012-10-24-imagej-conference.odp slides]
 +
|-
 +
| colspan=5 class="section-major" | '''[[ISBI 2012|Bioimage analysis workshop - ISBI 2012]]'''
 +
|-
 +
| 2012-Apr-30
 +
| {{Person|Rueden}}
 +
| ImageJ2 – ImageJ for the Next Generation of Biological Image Data
 +
|
 +
[http://bigwww.epfl.ch/eurobioimaging/presentation-rueden.pdf slides],
 +
[http://bigwww.epfl.ch/eurobioimaging/abstracts/rueden.pdf abstract]
 +
|-
 +
| colspan=5 class="section-major" | '''[[Conference 2010|2010 ImageJ Conference]]'''
 +
|-
 +
| 2010-Oct-27
 +
| {{Person|Rueden}}
 +
| ImageJDev: Next Generation ImageJ
 +
|
 +
[http://conference.imagej.net/2010/curtis-rueden/2010-10-27-ImageJDev.pdf slides]
 +
|-
 +
| colspan=5 class="section-major" | '''Other presentations'''
 +
|-
 +
| 2015-Jan-12
 +
| {{Person|Schindelin}}
 +
| The ImageJ Ops Framework: Image processing made easy
 +
|
 +
[https://imagej.github.io/presentations/2015-01-12-imagej-ops/ slides]
 +
|-
 +
| 2014-Mar-20
 +
| {{Person|Schindelin}}
 +
| SciJava Common: Plugins, Contexts, Utilities and More
 +
|
 +
[http://scijava.org/scijava-common/scijava-common.html slides]
 
|-
 
|-
| colspan=5 style="background: lightgray; text-align: center; padding: 0 !important" | Workshops
+
| 2010-Apr-06
 +
| {{Person|Rueden}}
 +
| ImageJ2: Directions & Goals
 +
|
 +
[https://imagej.github.io/presentations/2010-04-06-loci-imagej2-plan.pdf slides]
 +
|-
 +
| 2010-Apr-01
 +
| {{Person|Rueden}}
 +
| LOCI, Fiji & ImageJ2
 +
|
 +
[https://imagej.github.io/presentations/2010-04-01-loci-fiji-imagej2.pdf slides]
 +
|}
 +
 
 +
== Workshops ==
 +
 
 +
{| class="program"
 +
! '''Date'''
 +
! '''Presenter'''
 +
! '''Title'''
 +
! '''Resources'''
 +
|-
 +
| colspan=5 class="section-major" | '''[http://eubias.org/NEUBIAS/neubias2020-conference/symposium2017-lisbon/ 2017 NEUBIAS2020]'''
 +
|-
 +
| -
 +
| {{Person|Rueden}}
 +
| Scripting in ImageJ - An introduction to ImageJ Ops
 +
|
 +
[http://imagej.github.io/presentations/2017-02-12-imagej-ops-neubias/ slides]
 +
|-
 +
| colspan=5 class="section-major" | '''[[Conference 2015|2015 ImageJ Conference]]'''
 
|-
 
|-
 
| 2015-Sep-03
 
| 2015-Sep-03
Line 86: Line 303:
 
|
 
|
 
[https://vimeo.com/140929692 video],
 
[https://vimeo.com/140929692 video],
 +
[[Conference 2015 Program#Aryeh_Weiss1.2C2_-_An_introduction_to_digital_image_processing|abstract]],
 
[http://conference.imagej.net/2015/aryeh-weiss/IntroImageProcessingB.ppt slides],
 
[http://conference.imagej.net/2015/aryeh-weiss/IntroImageProcessingB.ppt slides],
[[Conference 2015 Program#Aryeh_Weiss1.2C2_-_An_introduction_to_digital_image_processing|abstract]]
+
[http://conference.imagej.net/2015/aryeh-weiss/stk_0001_Result%20of%20cftr-wt1.avi.zip data]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|BioVoxxel}}
 +
| Image processing, feature extraction and analysis using the BioVoxxel Toolbox
 +
|
 +
[https://vimeo.com/140929696 video],
 +
[[Conference 2015 Program#Jan_Brocher_-_Image_processing.2C_feature_extraction_and_analysis_using_the_BioVoxxel_Toolbox|abstract]],
 +
[https://www.dropbox.com/s/iurb5he4qpsqfrn/BioVoxxel%20Workshop.pdf?dl=0/ slides]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|Tiago}}
 +
| Scripting with BAR
 +
|
 +
[https://vimeo.com/140099767 video],
 +
[[Conference 2015 Program#Tiago_Ferreira_-_Scripting_with_BAR|abstract]]
 +
|-
 +
| 2015-Sep-03
 +
| Dominik Lindner<br>Petr Walczysko
 +
| The OMERO platform for management of microscopy data and beyond
 +
|
 +
[https://vimeo.com/140099766 video],
 +
[[Conference 2015 Program#Dominik_Lindner_and_Petr_Walczysko_-_The_OMERO_platform_for_management_of_microscopy_data_and_beyond|abstract]]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|Fab14}}<br>Stephane Dallongeville
 +
| Hands on Icy !
 +
|
 +
[https://vimeo.com/140929698 video],
 +
[[Conference 2015 Program#Fabrice_de_Chaumont_and_Stephane_Dallongeville_-_Hands_on_Icy_.21|abstract]]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|thewtex}}
 +
| SimpleITK
 +
|
 +
[https://vimeo.com/140099763 video],
 +
[[Conference 2015 Program#Matt_McCormick_-_SimpleITK|abstract]],
 +
[http://bit.ly/1hD5FZF interactive]
 
|-
 
|-
 
| 2015-Sep-04
 
| 2015-Sep-04
| [[User:Rueden|Curtis Rueden]] and {{Dev | id=bnorthan}}
+
| {{Person|Rueden}}<br>{{Person|bnorthan}}
 
| ImageJ2 scripts: Parameters + ImageJ Ops
 
| ImageJ2 scripts: Parameters + ImageJ Ops
 
|
 
|
 
[https://vimeo.com/140098817 video 1],
 
[https://vimeo.com/140098817 video 1],
 
[https://vimeo.com/140098835 video 2],
 
[https://vimeo.com/140098835 video 2],
[https://imagej.github.io/presentations/2015-09-04-imagej2-scripting/ slides],
+
[[Conference 2015 Program#Curtis_Rueden_and_Brian_Northan_-_ImageJ2_scripts:_parameters_.2B_ImageJ_Ops|abstract]],
[[Conference 2015 Program#Curtis_Rueden_and_Brian_Northan_-_ImageJ2_scripts:_parameters_.2B_ImageJ_Ops|abstract]]
+
[https://imagej.github.io/presentations/2015-09-04-imagej2-scripting/ slides]
 
|-
 
|-
| colspan=5 style="background: lightsteelblue; text-align: center; padding: 0 !important" | '''[[Conference 2012|2012 ImageJ Conference]]'''
+
| 2015-Sep-04
|-
+
| {{Person|Bio7}}
| 2012-Oct-24
+
| Statistical image analysis and reproducible reports with ImageJ and R
| [[User:Rueden|Curtis Rueden]]
 
| ImageJ2
 
 
|
 
|
[http://conference.imagej.net/2012/curtis-rueden/2012-10-24-imagej-conference.odp slides]
+
[https://vimeo.com/140098838 video],
 +
[[Conference 2015 Program#Marcel_Austenfeld_-_Bio7_.E2.80.93_Statistical_image_analysis_and_reproducible_reports_with_ImageJ_and_R|abstract]]
 
|-
 
|-
| colspan=5 style="background: lightsteelblue; text-align: center; padding: 0 !important" | '''[[Conference 2010|2010 ImageJ Conference]]'''
+
| colspan=5 class="section-major" | '''Other workshops'''
 
|-
 
|-
| 2010-Oct-27
+
| -
| [[User:Rueden|Curtis Rueden]]
+
| [[BioDIP]]
| ImageJDev
+
| Basics of Quantitative Image Analysis
 
|
 
|
[http://conference.imagej.net/2010/curtis-rueden/2010-10-27-ImageJDev.pdf|slides]
+
[http://workshops.imagej.net/Basics-of-Quantitative-image-analysis.pdf slides (PDF)]
 
|-
 
|-
| colspan=5 style="background: lightsteelblue; text-align: center; padding: 0 !important" | '''Other presentations'''
+
| 2015-Nov-03
 +
| [[LOCI]]
 +
| Intro to ImageJ Ops - Usage and Development
 +
|
 +
[http://workshops.imagej.net/IntroToOps.pdf slides (PDF)],
 +
[http://workshops.imagej.net/IntroToOps.pptx slides (PPT)]
 
|-
 
|-
| 2015-Jan-12
+
| 2016-Nov-17
| [[User:Schindelin|Johannes Schindelin]]
+
| [http://imagej.net/User:Iarganda Ignacio Arganda-Carreras]
| The ImageJ Ops Framework: Image processing made easy
+
| Introduction to Image Segmentation using ImageJ/Fiji
 
|
 
|
[https://imagej.github.io/presentations/2015-01-12-imagej-ops/ slides]
+
[http://imagej.net/_images/8/87/Arganda-Carreras-Segmentation-Bioimage-course-MDC-Berlin-2016.pdf slides (PDF)]
 
|}
 
|}
  
== See also ==
+
== Posters ==
  
* The ImageJ [[Conference 2015 Program]] page includes links to presentations from that conference, all of which relate to ImageJ in some way.
+
{| class="program"
 +
! '''Date'''
 +
! '''Presenter'''
 +
! '''Title'''
 +
! '''Resources'''
 +
|-
 +
| colspan=5 class="section-major" | '''[[Conference 2015|2015 ImageJ Conference]]'''
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|Iarganda}}
 +
| Trainable Weka Segmentation: a tool for machine-learning-based image segmentation
 +
|
 +
[[Conference 2015 Program#Ignacio_Arganda-Carreras_-_Trainable_Weka_Segmentation:_a_tool_for_machine-learning-based_image_segmentation|abstract]],
 +
[http://conference.imagej.net/2015/ignacio-arganda-carreras/poster-TWS-ImageJ-Conf-2015.pdf poster]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|BioVoxxel}}
 +
| The BioVoxxel Toolbox
 +
|
 +
[[Conference 2015 Program#Jan_Brocher_-_The_BioVoxxel_Toolbox|abstract]],
 +
[https://www.dropbox.com/s/7e6bjh3iqnxv014/IJcon2015-Poster%20Brocher%20%28150dpi%29.png?dl=0 poster]
 +
|-
 +
| 2015-Sep-03
 +
| Olaya Fernandez-Gayol
 +
| Using the wrMTrck plugin to analyze the Morris Water maze in mice
 +
|
 +
[[Conference 2015 Program#Olaya_Fernandez-Gayol_-_Using_the_wrMTrck_plugin_to_analyze_the_Morris_Water_maze_in_mice|abstract]],
 +
[https://dl.dropboxusercontent.com/u/21343536/Fernandez%20Gayol%20O.pptx poster]
 +
|-
 +
| 2015-Sep-03
 +
| David Logan
 +
| The ImageJ-CellProfiler Interface
 +
|
 +
[[Conference 2015 Program#David_Logan_-_The_ImageJ-CellProfiler_Interface|abstract]],
 +
[http://www.broadinstitute.org/~dlogan/posters/2015_09_03_ImageJ_Conf_DLogan_FINAL.pptx poster]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|Pietzsch}}
 +
| BigDataViewer&#8212;Visualization and Image Processing for Terabyte Data Sets
 +
|
 +
[[Conference 2015 Program#Tobias_Pietzsch_-_BigDataViewer.E2.80.94Visualization_and_Image_Processing_for_Terabyte_Data_Sets|abstract]],
 +
[https://www.dropbox.com/s/3st8ezbj9jmjzd8/bdv-poster-imagej2015.pdf?dl=0 poster]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|Saalfeld}}
 +
| ImgLib2 for visualization and generic image processing
 +
|
 +
[[Conference 2015 Program#Stephan_Saalfeld_-_ImgLib2_for_visualization_and_generic_image_processing|abstract]],
 +
[https://www.dropbox.com/s/f23tr3q607dxvlh/imglib2-imagej2015.pdf?dl=0 poster]
 +
|-
 +
| 2015-Sep-03
 +
| Raghavender Sahdev
 +
| TimeLapseReg – An ImageJ plugin for drift correction of video sequence in time-lapse microscopy
 +
|
 +
[[Conference 2015 Program#Raghavender_Sahdev_-_TimeLapseReg_.E2.80.93_An_ImageJ_plugin_for_drift_correction_of_video_sequence_in_time-lapse_microscopy_2|abstract]],
 +
[http://www.raghavendersahdev.com/uploads/3/9/6/2/39623741/timelapsereg.pdf poster]
 +
|-
 +
| 2015-Sep-03
 +
| {{Person|Twagner}}
 +
| Tools and methods of the Biomedical Imaging Group for ImageJ: An Overview
 +
|
 +
[[Conference 2015 Program#Thorsten_Wagner_-_Tools_and_methods_of_the_Biomedical_Imaging_Group_for_ImageJ:_An_Overview|abstract]],
 +
[https://dl.dropboxusercontent.com/u/560426/imagej/conference2015/poster.pdf poster]
 +
|}

Revision as of 09:49, 16 August 2017

Learn
Topics
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Presentations
Plugins
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Overview
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Running headlessly
Comparisons
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Multithreading in JavaScript
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Languages
BeanShell
Groovy
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JavaScript
Lisp (Clojure)
MATLAB
Python (Jython)
R (Renjin)
Ruby (JRuby)
Scala

Living workshops

These materials are regularly updated, and intended to teach ImageJ and Fiji at introductory, intermediate and advanced levels. The LOCI group uses them to teach ImageJ at the AQLM course every year, as well as locally.

Title Resources
Fiji-intro-slide.png Introduction to Fiji slides, video
Segmentation in Fiji slides, video
Scripting with Fiji slides, video

Talks

Date Presenter Title Resources
2017 NEUBIAS2020
2017-Feb-16 Curtis Rueden What's New in ImageJ2 ?

slides

2015 ImageJ Conference
Keynotes
2015-Sep-03 Wayne Rasband Introduction to ImageJ

video

2015-Sep-03 Curtis Rueden ImageJ2 and Fiji: The ImageJ2 platform, and the Fiji distribution of ImageJ

video, slides

2015-Sep-04 Mark Tsuchida Microscope control and image acquisition with Micro-Manager

video

2015-Sep-04 Florian Jug Getting stuff done – Software synergy with ImageJ + KNIME

video

Featured presentations
2015-Sep-04 Pariksheet Nanda Sharing the value of software freedom with non-programmers

video, abstract, transcript

2015-Sep-04 Tiago Ferreira Alternative approaches for neuronal morphometry

video, abstract

2015-Sep-03 John Bogovic The Thin Plate Spline method for smooth non-rigid transformations

video, abstract, slides

Lightning talks
2015-Sep-04 Anne Alerding Quantifying soybean stem tissues using common tools in ImageJ & Fiji

video, abstract

2015-Sep-03 Fabrice de Chaumont Yet another ImageJ friend: Icy

video, abstract

2015-Sep-03 Jesus Manuel Falagan Plugins to import, visualize, process & write astronomical FITS files

video, abstract

2015-Sep-04 Bill Heeschen Quantitative characterization of cellular irregularities in extruded polystyrene foam using digital image processing and analysis

video, abstract, macro,
slides (PDF), slides (PPTX)

2015-Sep-03 Mark Hiner ImageJ+MATLAB: Reunited

video, abstract, slides

2015-Sep-04 Irene Landrum SWAMP – a no-cost, open, high-performance computing platform for continuous software assurance

video, abstract, slides

2015-Sep-03 Melissa Linkert OME Bio-Formats: 10 years of proprietary image data

video, abstract, slides

2015-Sep-03 Michael Majurski Accurate and scalable Microscopy Image Stitching Tool (MIST)

video, abstract

2015-Sep-04 Benjamin Nanes Slide Set: Simplified batch processing with ImageJ2

video, abstract

2015-Sep-04 Brian Northan Flexible Deconvolution using ImageJ Ops

video, abstract, slides

2015-Sep-04 Stephan Saalfeld Seamless stitching without blending

video, abstract

2015-Sep-04 Raghavender Sahdev TimeLapseReg – An ImageJ plugin for drift correction of video sequence in time-lapse microscopy

video, abstract

2015-Sep-04 Benjamin Schmid Real-time multi-view deconvolution of time-lapse data on the GPU

video, abstract

2015-Sep-04 Amitabh Verma Acquisition, processing & re-processing using OpenPolScope plugin for Micro-Manager

video, abstract

2015-Sep-04 Thorsten Wagner NanoTrackJ – An open-source multi-modal size characterization tool for nanoparticle tracking analysis based on ImageJ

video, abstract, slides

2015-Sep-04 Petr Walczysko The Open Microscopy Environment (OME)

video, abstract

2015-Sep-04 Jay Warrick JEX – a platform for data management and batch processing with standard tools

video, abstract

2015-Sep-03 Aryeh Weiss Automated processing of telomeres with ImageJ and R

video, abstract, slides

2012 ImageJ Conference
2012-Oct-24 Curtis Rueden ImageJ2: Current Status and Future Directions

slides

Bioimage analysis workshop - ISBI 2012
2012-Apr-30 Curtis Rueden ImageJ2 – ImageJ for the Next Generation of Biological Image Data

slides, abstract

2010 ImageJ Conference
2010-Oct-27 Curtis Rueden ImageJDev: Next Generation ImageJ

slides

Other presentations
2015-Jan-12 Johannes Schindelin The ImageJ Ops Framework: Image processing made easy

slides

2014-Mar-20 Johannes Schindelin SciJava Common: Plugins, Contexts, Utilities and More

slides

2010-Apr-06 Curtis Rueden ImageJ2: Directions & Goals

slides

2010-Apr-01 Curtis Rueden LOCI, Fiji & ImageJ2

slides

Workshops

Date Presenter Title Resources
2017 NEUBIAS2020
- Curtis Rueden Scripting in ImageJ - An introduction to ImageJ Ops

slides

2015 ImageJ Conference
2015-Sep-03 Aryeh Weiss An introduction to digital image processing

video, abstract, slides, data

2015-Sep-03 Jan Brocher Image processing, feature extraction and analysis using the BioVoxxel Toolbox

video, abstract, slides

2015-Sep-03 Tiago Ferreira Scripting with BAR

video, abstract

2015-Sep-03 Dominik Lindner
Petr Walczysko
The OMERO platform for management of microscopy data and beyond

video, abstract

2015-Sep-03 Fabrice de Chaumont
Stephane Dallongeville
Hands on Icy !

video, abstract

2015-Sep-03 Matt McCormick SimpleITK

video, abstract, interactive

2015-Sep-04 Curtis Rueden
Brian Northan
ImageJ2 scripts: Parameters + ImageJ Ops

video 1, video 2, abstract, slides

2015-Sep-04 Marcel Austenfeld Statistical image analysis and reproducible reports with ImageJ and R

video, abstract

Other workshops
- BioDIP Basics of Quantitative Image Analysis

slides (PDF)

2015-Nov-03 LOCI Intro to ImageJ Ops - Usage and Development

slides (PDF), slides (PPT)

2016-Nov-17 Ignacio Arganda-Carreras Introduction to Image Segmentation using ImageJ/Fiji

slides (PDF)

Posters

Date Presenter Title Resources
2015 ImageJ Conference
2015-Sep-03 Ignacio Arganda-Carreras Trainable Weka Segmentation: a tool for machine-learning-based image segmentation

abstract, poster

2015-Sep-03 Jan Brocher The BioVoxxel Toolbox

abstract, poster

2015-Sep-03 Olaya Fernandez-Gayol Using the wrMTrck plugin to analyze the Morris Water maze in mice

abstract, poster

2015-Sep-03 David Logan The ImageJ-CellProfiler Interface

abstract, poster

2015-Sep-03 Tobias Pietzsch BigDataViewer—Visualization and Image Processing for Terabyte Data Sets

abstract, poster

2015-Sep-03 Stephan Saalfeld ImgLib2 for visualization and generic image processing

abstract, poster

2015-Sep-03 Raghavender Sahdev TimeLapseReg – An ImageJ plugin for drift correction of video sequence in time-lapse microscopy

abstract, poster

2015-Sep-03 Thorsten Wagner Tools and methods of the Biomedical Imaging Group for ImageJ: An Overview

abstract, poster