We have a facility YouTube channel where we host how-to videos. Follow our channel or check out the videos embedded below. We also save playlists created by other people or organisations that you may find useful.

If there’s something you would like to see added to this page, let us know via the suggestion box at the bottom of this page.

Click the links below to skip to the category of videos.

ImageJ/FIJI videos

Imaris videos

Micro-Manager videos

QuPath videos

CellProfiler videos

FIJI/ImageJ videos

Setting scale and adding a scale bar in ImageJ.

The document with the scaling relevant to the IGC AIR microscopes can be found on the Technical Specifications Page.

Changing channel colours in ImageJ.

Watch this video to find out about changing lookup tables for your multi-channel images in ImageJ.

Splitting and merging channels in ImageJ

Introduction to the channels tool in ImageJ.

This useful tool can be used to easily switch between viewing your channels separately or together.

How to show images with the same display values

How to propogate the same minimum and maximum values to a series of images to compare your conditions.

Making a simple montage in ImageJ

Creating a intensity profile plot in ImageJ.

The plot profile tool in ImageJ can be used to create a plot of intensity values across features in your image.

One of the macros created in the facility will take your Micro-Manager images and save them as RGB for display. This video demonstrates how to use that macro which can be found on our Github.

Imaris Videos

Making a simple movie in Imaris

Micro-Manager videos

How to setup μManager

Most of the epifluoresence microscopes use μManager for acquisition. This video shows you to initially configure μManager the first time you log on to a new microscope.

Tiling with μManager

How to set up a tiling acquisition and then stitch the image once acquisition is complete.

QuPath videos
CellProfiler videos

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