Labelling objects in a picture with numbers

Question

I need help processing a biology bacteria picture. I just started learning Mathematica and I hope you guys can use a simple method to help me solve the problem, please do not use super complicated methods.

Below is what I want to do, it was done by my friend and he refuses to teach me. I want to label each bacteria cell on the picture with numbers.

My thoughts are as follows:

1. Binarize the image and use ComponentMeasurements to find the centroids of all bacteria cells.
2. Convert the centroids (coordinates) to numbers 1 to 12 and make it into a graphic.
3. Show my original picture together with the picture numbered 1 to 12 to get my end result.

However, my problem is that I do not know how to convert centroids (which are coordinate positions) into numbers.

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Thanks Simon Woods! Here is my code and my attempt. Please correct me and see which part am I wrong.

Firstly, This is the picture I started off with (named "bacteria") and I want it to be labelled as shown on the above picture.

And this is my code. I did not include how I sharpen and binarize the picture because it is quite straightforward. I will only start with the part whereby I get the centroids. i named my binarized picture as "image".

morpData = MorphologicalComponents[image]
Tally@Flatten@morpData
cenData = ComponentMeasurements[morpData, {"Centroid"}]
getCenData = centroidData[[All, 2, 1]]

After these 4 steps, I managed to get the list of centroid coordinates which are

{{483.727, 478.227}, {422., 442.5}, {289.862, 331.534}, {245.261, 299.542}, {140.959, 259.041}, {404.427, 224.821}, {538.261, 223.39}, {56., 174.192}, {41., 140.844}, {190.529, 95.6238}, {277.262, 65.4048}, {491.833, 34.2778}}

This is good because I managed to identify all 12 bacteria in the picture. However, I need to know how to convert centroid coordinates to labeled numbers!!

I tried, but I still cannot do it. And to prove that I really tried, this is my latest effort at trying to convert the 12 centroid coordinates into numbering and overlay with the original image. Please tell me where I went wrong:

Show[bacteria,Map[Graphics[Text[Style[getCenData[[1]], Red], getCenData[[2]]]], getCenData]]

And please, do not tell me to convert one by one, that is too troublesome.

Answer 1

You are most of the way there! Here is the setup: import the image and binarize, then get the locations of the centroids of the components (the positions of the bacteria).

img = Import["https://i.sstatic.net/Xj143.jpg"];
binImg = Dilation[Binarize[img, 2/3], 5];
centroidData = ComponentMeasurements[binImg, {"Centroid"}]
getCenData = centroidData[[All, 2, 1]];

All that remains is to plot and superimpose the numbers:

Show[Image[img, ImageSize -> 600], 
Graphics[{Red, Table[Inset[ToString[i], getCenData[[i]]], {i, 1, Length[getCenData]}]}]]

Answer 2

You haven't posted the code you already have, nor a source image so we can reproduce your results (and see where you're stuck), so you won't get a full answer to your question. Consider this a long comment.

Your seem to have 4 separate questions:

1. How do I find the cells?
2. How do I draw something?
3. How do I draw something over my microscope image?
4. How do I draw the cell indices at the positions where I found the cells?

As far as I understand, you've already solved the first question. I'll assume you have a list of rules like 1 -> {100,200}, 2 -> {110,250}, 3 -> ..., and have this list assigned to a variable called e.g. cellLocations.

The answer to question 2 is the built-in function Graphics: Graphics takes a list of graphics primitives like lines, circles, text objects, colors, fill styles and so on, and renders them. For example:

Graphics[{Red, Line[{{10, 10}, {20, 20}}], Text["Hello World", {20, 20}]}]

draws a red line and a line of text. Read the documentation on graphics carefully if you want to draw anything more complex than a straight line.

The answer to question 3 is the built-in function Show: You can use it to render a graphics object in front of an image object, like this:

Show[myImage, Graphics[{ ... }]

Finally, the last question: how do you turn a list of cell locations in some format (as returned by ComponentMeasurements) into a list of graphics primitives? As @David Carraher explained in a comment: Mathematica's Replace function (or it's short form /.) is very useful for that. Be sure to read the documentation, too.

Finally, a word of advice: Mathematica is perfectly suited for what you're trying to do, but piecing it together by trial and error, documentation and stackexchange is bound to be frustrating. (At least, it was for me.) Do yourself a favor and get a good introductory book. It'll save you a lot of time, and possibly a few gray hairs, too.