@Maria

Out of curiosity I just modifiied the Macro. It is now adding time stamps to the lower right corner. Just a very quick and dirty solution. But maybe it helps. You must run it under Fiji or ImageJ+the LOCI bioformats plugin.

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// TimeStamp.ijm

// Written by Arne Seitz; based on a Macro from Curtis Rueden (planeTimings.txt)

// Last updated on 2013 April 17

// Uses Bio-Formats to print the chosen file's plane timings to the Log.

run("Bio-Formats Macro Extensions");

id = File.openDialog("Choose a file");

print("Image path: " + id);

open(id);

w=getWidth;

h=getHeight;

run("RGB Color");

run("Colors...", "foreground=red background=green selection=orange");

Ext.setId(id);

Ext.getImageCount(imageCount);

print("Plane count: " + imageCount);

creationDate = "";

Ext.getImageCreationDate(creationDate);

print("Creation date: " + creationDate);

deltaT = newArray(imageCount);

exposureTime = newArray(imageCount);

print("Plane deltas (seconds since experiment began):");

for (no=0; no

1. It is not clear, that you want the time frame information as in which format, as text or as number.

2. For multiple operations i think there is Batch commanding (Macro) in ImageJ though it needs a basic level of programming. But it is there.

I feel this is a similar conversation in an external blog.

http://imagej.1557.x6.nabble.com/extracting-acquistion-times-from-time-series-td3682313.html

You can use the metadata of the image in order to create the time-stamps if they are stored correctly. Extraction of the them will work via the following macro/program form the LOCI consortium. If you are able to extract the time information correctly with one of these tools it is rather straight foreward to write them to your images (e.g. with a little macro).

For an ImageJ macro, see planeTimings.txt, linked from:

http://loci.wisc.edu/bio-formats/imagej

For Java code, see PrintTimestamps.java, linked from:

http://loci.wisc.edu/bio-formats/bio-formats-java-library

I think you need a ImageJ plugin: time stamper. Let me know if you need help with that.

Did you looked at pluggin time series analyser ??

@Richa: "This plugin is built into ImageJ 1.43t and later as the Image>Stacks>Label command." This is what I used.

@Saurabh: The time should be given as number in one corner of the video, e.g. 00:00, 00:10, .... 12:00.

@Arne: I think I understand what you suggest doing. I have never used macros before and will have to do some reading on how to do this.

@Joan: Yes, I did look at TimeSeriesAnalyzer, but didn't find any function that does this?

Can you set up the instrument to save the time information? This way each individual movie will have its unique time stamps.

For example .ND2 files used by Nikon microscopes have full imaging configurations stored, for each movie, including laser used, intensity and camera gains.

Agreeing with Nehad, every acquisition software should have the time display option on the video. Enabling that option prior to exporting the video might work. I use Zeiss Zen software for all my videos and it has plenty of such options.

How about using "Time Stamper"? I know the following works with Fiji (http://fiji.sc):

1. Open your stack

2. Type CTRL-L (on MS Windows machine) or Command-L (in OS X) to invoke the "Command Finder"

3. Type "Time Stamper", select it and then click "Run"

4. Simply enter the time interval and time units In the user interface that shows up

Here is a script for you to play with. Save the following as a "test.ijm" and open it (drag and drop) in Fiji. Maybe it will help... :

newImage("Test_stack", "8-bit Black", 512, 512, 13);

run("Time Stamper", "starting=0 interval=1 x=2 y=15 font=12 decimal=0 anti-aliased or=sec");

run("Time Stamper", "starting=1 interval=1 x=2 y=35 font=12 decimal=0 anti-aliased or=sec");

@ Miso: Probably, Maria needs a tool that automatically extracts timestamps from file metadata.

@Gaetano: yes, this would be ideal. However, without knowing the file format/software that generated the file and knowing the interval she mentioned, I felt the script might be helpful.

@Maria

Out of curiosity I just modifiied the Macro. It is now adding time stamps to the lower right corner. Just a very quick and dirty solution. But maybe it helps. You must run it under Fiji or ImageJ+the LOCI bioformats plugin.

---------------------------------------------------------------------------------------------------------------

// TimeStamp.ijm

// Written by Arne Seitz; based on a Macro from Curtis Rueden (planeTimings.txt)

// Last updated on 2013 April 17

// Uses Bio-Formats to print the chosen file's plane timings to the Log.

run("Bio-Formats Macro Extensions");

id = File.openDialog("Choose a file");

print("Image path: " + id);

open(id);

w=getWidth;

h=getHeight;

run("RGB Color");

run("Colors...", "foreground=red background=green selection=orange");

Ext.setId(id);

Ext.getImageCount(imageCount);

print("Plane count: " + imageCount);

creationDate = "";

Ext.getImageCreationDate(creationDate);

print("Creation date: " + creationDate);

deltaT = newArray(imageCount);

exposureTime = newArray(imageCount);

print("Plane deltas (seconds since experiment began):");

for (no=0; no

Thanks to everybody, you all gave very helpful answers.

@Arne: It's very kind of you to provide the code, I will try it during the next days!

NIS viewer allows you access to all image metadata, and provides functionality to export this information. However this cannot be automated...

There is the option of using cellprofiler which can extract quite a bit of metadata information automatically, but sadly does not extract the time info. What's promising is that cellprofiler can be run from python. So, in my free time i will be exploring the metadata import module.

Python has an nd2reader module you can install this from the anaconda prompt by typing

pip install nd2reader

You can then call this into your script as,

import nd2reader

and then use it as

video = nd2reader.ND2Reader("yourfile.nd2")

This will then have a variety of attribute you can observe and export. The time information you asked for can be accessed as

time_information = video.timesteps

print(time_information, file=open('myfile.txt', 'w'))