Fiji-ImageJ

ImageJ-Fiji can be downloaded from here. It does not require installation (at least on Mac), the application runs directly from the executable. Unzip the file to a directory, double click the application, and Fiji toolbar will appear on the screen.

Colony Count

We shall start with this image shown here on left to perform a colony count estimation.

Cell Counting to Cell Segmentation

You can use the image from here to try out this analysis.

In the following we shall see how counting can be done as before by using the output of Step III. Further next we shall show the segmentation task by proceeding from the same output of Step III.

We shall study the cell segmentation task now.

You can save the statistics in a CSV file for creating nice plots with your favorite graph plotter. Let us move to the next task. This image is little bit on a cleaner side. What happens when the image has more clubbing with lot more cells touching each other and with higher level of noise? Let us experiment with this image.

Image Annotations with Fiji-ImageJ

Those of you who wish to do machine learning with your acquired images will also need to annotate the images to train your machine learning algorithm. How to annotate the image will depend on the fundamental visual recognition task you are trying to solve. In the following you shall see some cool Fiji tools to annotate your images pretty fast: from detection to segmentation to even tracking, you can do your annotation using Fiji.

Detection

One can use the point tools to mark the desired locations (e.g., nuclei centers if you are interested in detecting nuclei centers). You can get the list of all teh marked centers either via ROI Manager or Measure as shown.

Tracking

One can annotate the extracted frames (use the ffmpeg tool to extract frames from video) with Fiji plug in MTrackJ.

Segmentation Masks

The left side shows how you can use the polygon tool to create a closed loop contour around the cellular object. Once done you need to add the contour to ROI Manager, otherwise you are going to lost the contour. Once you add the contour you can go to making the next one. When all contours are made, select all with shift + click all, and click More on ROI Manager to apply Fill operation. Next go to Image > Adjust > Threshold to select the segmentation mask.

Page updated

Google Sites

Report abuse