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Image J workshop 2019 material PDF
Written by Yannick KREMPP   
Monday, 17 June 2019


As requested by the workshop attendees, here are the PDFs of the talk and the demo outline for those who want to reproduce some of the steps I have demoed onstage.



Here's also some of the macros used to process the demo sample (save them as a *.ijm file to use them in FIJI):

Converting a large image to a stack of smaller tiles :

macro "create stack of tiles [s]" { // run("RGB Color"); //ask for user input n = getNumber("How many divisions?", 2); id = getImageID(); title = getTitle(); getLocationAndSize(locX, locY, sizeW, sizeH); width = getWidth(); height = getHeight(); tileWidth = width / n; tileHeight = height / n; newImage("TilesStack", "RGB composite-mode", tileWidth, tileHeight, 1, n*n, 1); idStack = getImageID(); for (y = 0; y < n; y++) { offsetY = y * height / n; for (x = 0; x < n; x++) { offsetX = x * width / n; selectImage(id); call("ij.gui.ImageWindow.setNextLocation", locX + offsetX, locY + offsetY); tileTitle = "title="+ title + " [" + x + "," + y + "]"; makeRectangle(offsetX, offsetY, tileWidth, tileHeight); run("Copy"); selectImage(idStack); run("Paste"); run("Next Slice [>]"); } } selectImage(id); close(); }

Processing a tile :

macro "Filter image and Analyze [f]" { // Make sure you don't touch the original image - useful for batch processing run("Duplicate...", "Copy of original image"); run("RGB Color"); // Ask for user input medianRadius = getNumber("Type in the median radius: ", 2); // Do the segmentation run("Median...", "radius=" + medianRadius); run("Color Threshold..."); // Color Thresholder 2.0.0-rc-68/1.52h // Autogenerated macro, single images only! min = newArray(3); max = newArray(3); filter = newArray(3); a = getTitle(); run("HSB Stack"); run("Convert Stack to Images"); selectWindow("Hue"); rename("0"); selectWindow("Saturation"); rename("1"); selectWindow("Brightness"); rename("2"); min[0] = 145; max[0] = 184; filter[0] = "pass"; min[1] = 21; max[1] = 255; filter[1] = "pass"; min[2] = 170; max[2] = 255; filter[2] = "pass"; for (i = 0; i < 3; i++) { selectWindow("" + i); setThreshold(min[i], max[i]); run("Convert to Mask"); if (filter[i] == "stop") run("Invert"); } imageCalculator("AND create", "0", "1"); imageCalculator("AND create", "Result of 0", "2"); for (i = 0; i < 3; i++) { selectWindow("" + i); close(); } selectWindow("Result of 0"); close(); selectWindow("Result of Result of 0"); rename(a); // Colour Thresholding------------- //setThreshold(255, 255); setOption("BlackBackground", true); run("Make Binary"); // Clean the segmentation run("Median...", "radius=2"); run("Fill Holes"); run("Watershed"); // Specify what has to be measured and analyze run("Set Measurements...", "area perimeter redirect=None decimal=3"); run("Analyze Particles...", "size=50-Infinity display exclude clear add in_situ"); }


Yannick Krempp

Last Updated ( Monday, 17 June 2019 )
Workshops 2019 PDF
Written by Yannick KREMPP   
Friday, 10 May 2019

The schedule of the next series of workshops given by the CIF is now live :


These workshops are intended for max 15 pers. Registration (free) is recommended (mail to Jean-Yves Chatton ).

The students of the doctoral schools (neuroscience, FBM, etc.) can validate their participation to a workshop as one seminar for their credits.
Links to previous workshops content and documents:


Last Updated ( Friday, 10 May 2019 )
Welcome to our new collaborator, Luigi Bozzo ! PDF
Written by Yannick KREMPP   
Friday, 11 January 2019
This CIF platform is happy to welcome a new collaborator, Luigi Bozzo.

Here's a short bio about him:
Luigi Bozzo has a solid theoretical and practical knowledge in light microscopy accumulated over 10 years of experience. He started his career doing a PhD in neuroscience at UNIL on the functional interplay between neurons and glial cells. To gain access to spatial and temporal aspects of these dynamic interactions, he used optical microscopy, associated with specific fluorescent indicators on living tissues. 
Then he entered the world of core microscopy facilities as an ad interim technical manager at the CIF before being hired as microscopist at the Bioimaging and Optics Platform (BIOP), EPFL. He was dealing with all aspects of modern light microscopy in particular in the field of life sciences and was involved in all aspects of the core microscopy facility. He was exposed to different microscopy techniques like wide-field imaging, confocal imaging up to super resolution methods. In particular, he gained expertise in advanced techniques such as fluorescence life-time imaging microscopy (FLIM), Fluorescence Resonance Energy Transfer (FRET), Fluorescence recovery after photobleaching (FRAP), spectral unmixing, and intelligent image acquisition (fully automated acquisition workflow).

As technical manager/microscopist, he came in contact with scientists from very diverse backgrounds, from physics to medicine. He helped them by supporting their scientific projects; advising them on experimental designs; discussing staining strategies; choosing the appropriate microscope; providing assistance to obtain the optimal image acquisition and analysing the output. He successfully trained more than 400 users to the usage of microscopy systems.

Luigi Bozzo started on Dec. 1st 2018 as technical manager of the CIF AGORA/BUGNON facility branch. He will assist on the trainings on the Bugnon Campus as well as taking care of the new Agora CIF facility. He will also participate in every other activities of the CIF platform in general.
You can reach Luigi at: 

  • Office phone + 41 21 545 10 60 / + 41 79 556 95 52
  • Office address: Centre de recherche AGORA – Cellular Imaging Facility – Rue du Bugnon 25A – Bureau 248 CH 1011 Lausanne.
  • Email : This e-mail address is being protected from spam bots, you need JavaScript enabled to view it

Last Updated ( Friday, 11 January 2019 )
Workshops - Updated ! PDF
Written by Yannick KREMPP   
Wednesday, 29 August 2018
Next Workshops given by the CIF: Wednesdays between 12:15 and 14:00.
These workshops are intended for max 15 pers. Registration (free) is recommended (mail to Jean-Yves Chatton ).
The students of the doctoral schools (neuroscience, FBM, etc.) can validate their participation to a workshop as one seminar for their credits.
Links to previous workshops content and documents:
Last Updated ( Thursday, 08 November 2018 )
CIF WORKSHOPS - Imaris: The ideal solution to interactively analyze microscopy images by Geargie Gol PDF
Written by Yannick KREMPP   
Friday, 25 May 2018
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