Bioimage analysis with Icy

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# Bioimage analysis with Icy
## Webinar - NEUBIAS Academy <span class="citation">@Home</span>
### Marion Louveaux
### <p>Institut Pasteur, Paris</p>
<a href="https://marionlouveaux.github.io/bioimage_analysis_with_icy/" class="uri">https://marionlouveaux.github.io/bioimage_analysis_with_icy/</a>
### 2020-04-22

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      <a href="https://marionlouveaux.fr/">marionlouveaux.fr</a>
      <a href="https://twitter.com/MarionLouveaux">@MarionLouveaux</a>
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# Introduction     
        
- Icy, a bioimage analysis software bridging people accross disciplines           
- Protocols, making quantitative analyses accessible to everyone          
- Community, get involved!

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# Icy, a bioimage analysis software bridging people accross disciplines

Icy offers the means for 
- perform quantitative analyses in a reproducible manner, even without programming knowledge            
- get the latest image analysis and computer vision algorithms in an accessible manner         
- easily share bioimage analysis workflows with the very diverse bioimage analysis community

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# Protocols, making quantitative analyses accessible to everyone

Protocols offers the means for       
- automated processing without programming knowledge       
- flexibility required to achieve complex tasks      
- transparency and reproducibility

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# Community, get involved!

Icy is a community effort, relying on:     
- the existence and renewal/updating of resources      
- communication around these resources      
- sharing knowledge

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# Poll n°1

**Choose what applies to you most**           
- I do image analysis for my projects only     
- I do image analysis for the others only         
- I do image analysis for myself and for the others

**Your knowledge of Icy**
- I never heard about Icy     
- I heard about Icy but never used it      
- I used Icy it a couple of times         
- I used Icy many times

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# Outline

1. Icy, a bioimage analysis software bridging people accross disciplines                          
2. Protocols, making quantitative analyses accessible to everyone                 
3. Community, get involved!

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# Icy: The origins of the Icy software

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# Icy: The choice of a developed & unified GUI

> Image: SAM_PI_Col-0.tif, from http://doi.org/10.5281/zenodo.2577053

???
1. A unified graphical user interface       
      - No floating windows      
      - Unified plugins layout     
      - Condensed information (see the side pane)
2. Everything at your fingertips
      - Ribbon menu: quick access to basic operations & main plugins      
      - Side pane: display options, ROI manager with result table, overlays control, history and log window       
3. Make the software easier to use       
      - Search bar: access all tools, even if not yet installed
      - Direct access to online documentation & website     
      - Possibility to send bug reports and log files directly from the GUI

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# Icy: Display options & sequence properties        
         
<img src="images/GUIsidepane.png" width="5027" />

> Image: SAM_PI_Col-0.tif, from http://doi.org/10.5281/zenodo.2577053

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# Icy: Viewer options 
         
<img src="images/GUIviewer.png" width="5027" />

> Image: SAM_PI_Col-0.tif, from http://doi.org/10.5281/zenodo.2577053

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# Icy: Windows synchronization

![:col_row

]

> Image: SAM_PI_Col-0.tif, from http://doi.org/10.5281/zenodo.2577053

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# Icy: Results

> Image: image_1.tif, from https://zenodo.org/record/3706554#.XpgUbZk6-Uk

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# Icy identity: Code

<img src="images/Plugins.png" width="5027" />
> http://icy.bioimageanalysis.org/download/

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# Icy identity: Code

> http://icy.bioimageanalysis.org/plugins/

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# Icy: Highlighting some plugins

Counting spots with *Spot detector*

![:col_row Segmentation with <i>Active contours</i>, Tracking with <i>Track Manager</i>, Flow analysis with <i>BioFlow</i>]
![:col_row 
<img src="images/active_contours_video.gif" width="75%" />
,
<img src="images/221219-ICY-MOVIES - 25X 54 (crop)_TrackingAmoeba.gif" width="100%" />
,
<img src="images/bioflow_2D.gif" width="100%" />
]         
![:col_row Credits: D. Gaboriau, Credits: M. Manich, Boquet-Pujadas et al. (2017)]

> http://icy.bioimageanalysis.org/plugin/spot-detector/         
http://icy.bioimageanalysis.org/plugin/active-contours/          
http://icy.bioimageanalysis.org/plugin/track-manager/         
http://icy.bioimageanalysis.org/plugin/bioflow/

???
extract motion of intracellular material observed using fluorescence
microscopy, while simultaneously inferring the parameters of a given theoretical model 
actin bulk flow

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# Icy: 3D rotation plugin

![:col_row

<img src="images/3Drotationplugin.png" width="80%" />
,

<img src="images/3D rotated view of SAM_PI_Col-0_0ms.gif" width="100%" />
]

> http://icy.bioimageanalysis.org/plugin/3d-rotation/

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# Icy: Protocols

> http://icy.bioimageanalysis.org/protocol/3d-mouse-embryo-quantification/         
http://icy.bioimageanalysis.org/plugin/protocols/

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# Icy: Interoperability with other tools

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# Icy: Conclusions

- Unified graphical user interface       
- Large variety of plugins
- Graphical programming option

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# Questions?

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# Poll n°2

**The 1st part of this webinar has...**       
- ... triggered my interest for Icy     
- ... not quite raised my interest for Icy yet

**Protocols and graphical programming (not limited to Icy)**     
- I never heard about it    
- I already heard about it but never tried       
- I am familiar and have used it a couple of times          
- I use it often

**Your knowledge in at least one programming language**        
- zero programming knowlegde      
- basic knowlegde      
- intermediate knowlegde      
- advanced knowledge

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# Outline

1. Icy, a bioimage analysis software bridging people accross disciplines                           
2. Protocols, making quantitative analyses accessible to everyone                 
3. Community, get involved!

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# Protocols: Common issues

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# Protocols: Definition of bioimage analysis

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# Protocols: Example