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Life Science & Imaging  
  

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Inserm Trainings

Lydia Danglot is also a trainer at Inserm since 2013, she's teaching in three national trainings open to researchers, engineers, students and post-doc .

  • Training " From Microscope to final figures with the Adobe suite " : This course is designed to familiarize all scientists with different software for the design of scientificl figures based on images acquired microscope.
    A kind of " survival kit " in computer graphics for scientists :
    1. Introduction to image formats with free software ImageJ , Fiji or Icy .
    2. Conversion and image colorization with Photoshop : layers and text tools, compression and export in different formats ( JPG , TIF, EPS , PDF) .

     

    photoshop

    3. Build graphs, charts and posters with Illustrator
    Learn quickly how to handle drawings with the pen, bezier curves, vectorizing a scanned drawing.
    Edit graphics from Excel and GraphPad Prism .
    4. Layout of figures and arguments with " In Design "
    Create a figure without cutting raw images using dynamic links.
    Impose the export format ( 300/600 ppi resolution, RGB / CMYK, image size ) .
    Exchanges and compression with Adobe Acrobat.


  • Training " Microscopy and Image Analysis : Icy ImageJ " : This course is designed to introduce the scientific microscopy image analysis software that are free and available on every operating system (Mac, PC, Linux) .

Sort of a "toolbox" for image analysis in microscopy:
1. Introduction to image analysis:
Reminders on fluorescence, numerical aperture, LUT, image formats, regions of interest, 2D or 3D + time ...
QuickStart software: namely open and work the owners of images from microscopes formats with ImageJ software, Fiji or Icy.

2. Segmentation, detection and monitoring of biological objects (particles, cells and organisms)
Segmentation, thresholding wavelet detection, active contours enabling automatic tracking of cell deformation and / or migration.
Quantification in histology and fluorescence (color picker, scale bar, measurement and colocalizations, ...)
3. Automating tasks in Icy

Using the Icy protocols automation for graphical programming without any line of code. And for the most agile: Macros developed in Javascript.
4. Training with file management and quantification:
Practical exercises on images selected by trainers and taken by trainees, solving particular problems.

icy


Training " Icy Level 2 : spatiotemporal Analyses" This advanced training, deals with deconvolution techniques, spatial analysis (colocalization) and particle tracking over time.
- Brief segmentation reminders for the detection and monitoring of biological objects (Cells, organelles, vesicles, single molecules) thresholding detection
Wavelet, active contours, HK-Means.
- Preparing images or temporal sequences: crop 5D, registration and
deconvolution.
Deepening the spatial analysis tools
- Differences between colocalization and coupling.
- What methods to identify events
coupling between 2 or 3 channels?
- Spatial Statistical Analysis
- Evaluation of distances between multiple ROI (membrane organelles,
vesicles).
ICY NIVEAU2

Deepening the temporal analysis
- Tracking fluorescence over time in region of interest
- Dedicated and automatic export to Excel.
- Detection and tracking of particles / cells over time. Filtering tracks (depending on the duration, distance, displacement net). Visualization of trajectories in 2D or 3D.
- Identification of endocytosis and exocytosis events.
Automating
- Automation of tasks thanks to Icy protocols "friendly Macros" in graphic shapes to achieve these batch analyzes treatment.
- Rename and color the regions of interest before exporting datas in excel.
- Sort and Export data to excel in the case of batch processes.
- Case studies on images prepared by the trainers: the most common case (quantification colocalization, application of ROIs of a channel on another, particle count, ...).
- Case studies on the images of trainees and individual troubleshooting.

 

 

 
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