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How To Name Image Files So They Actually Make Sense – The Good, The Bad And The Ugly

Posted in: Microscopy and Imaging
How To Name Image Files So They Actually Make Sense - The Good, The Bad And The Ugly

I have a dear friend and collaborator whose image file names follow this format:




aaaa6p3kkkkkkk.tif, etc.

We have collaborated together on several projects, and I dread the days I have to go back through the files and look for a particular image. I am sure that these names have some meaning to her. For the life of me, I do not know what that meaning is!

It is an art

There is an art to naming files. If you are only going to be taking images on one day for one project, it may be ok to use names like, ‘goodcell.tif’. However, if you are like most of us, and will be recording a large number of images for different samples and projects, you’re going to need something which makes more sense when staring at a folder full of file names.

Think of the future

A good naming system describes the sample and the image in a way that is clear to you and others- both today and in the future. It also ensures that if the file is placed in the wrong folder you will still know what you are looking at.

Plan your system

In planning your naming system, first list the information which is important to your project and image.

Examples include:

– Date of experiment

– Sample (control, syt4 mutant, etc.)

– Slide or grid number

– Cell number

– Area of cell

– Imaging method (DIC, Fluorescence, etc.)

– Magnification

All this information is critical for me in my hypothetical experiment, so I will include all of it in my file name. The next question is: what order do I put the information in the file name? To answer this question you want to think about how the files will be listed on your computer later when you are looking for an image. If files are appearing as a list they will appear alphabetically- essentially grouped by whatever goes toward the beginning of the name.

EU vs US

I always start my names out with the factors that change the least often: the date, the sample and the slide/grid number.

For control slide 1 on April 6th, the name starts off as:


You will notice that I enter the date as year_month_day. This is typical for Europeans, but may appear odd for Americans (who are used to writing the day before the month). I am American, however, when I look through a large number of files from different days, I want the experiments to appear in the order in which they were conducted. This requires the year_month_day in numerical format.

Gets trickier…

After date_sample_slide, it gets trickier. Do you want all the 40x images grouped together, or, all the images from Cell #2? For my hypothetical experiment, I want to image different areas of the cell with both DIC and fluorescence, and when I go back through the images I want the matching DIC and fluorescence images to be together. Consequently, for a 40x DIC image of area ‘a’ of cell 1 I will write:




With these file names, I immediately know the date, the sample, the slide number, the cell number, the cell area, magnification and imagine technique. Should a file be placed in the wrong folder, it will be immediately clear to me from the file name and won’t lead to any data interpretation mistakes.

I’m not a mind reader you know

Since there can still be some ambiguity if someone else is looking for data (“did she list the day or the month first?!”), the final step is to write a key for the names in your lab notebook (along with the other details of the experiment). Better yet, include a file with a key in the folder with your data!

There you have it: image file names

the good (2013_04_06_controlS1Cell1_40xaDIC.tif)

the bad (goodcell.tif)

and the ugly (aaaa5kk.tif).

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  1. R J on October 26, 2016 at 10:10 pm

    “year_month_day. This is typical for Europeans, but may appear odd for Americans (who are used to writing the day before the month)”

    I’m not sure what you meant by this, that order is not typical for Europeans (who use DAY-MONTH-YEAR). You’re wrong about what Americans use too — they use MONTH-DAY-YEAR.

    Regardless the system you’re using is the best, ISO 8601.

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