Make EDF at each timepoint.

ajay_zalavadia

I am working with LIF file which has time-lapse data for different positions of the well plate. At each position for each time point I also have z-stacks. I open one position time series (also with z-stacks) to apply the EDF , it seem it only creates the EDF from the time point that is active in the viewer. Is it possible to cycle through each data set (positions) and create EDF for each time point. It would  be great if the result are retained as time serie.

YuriG

Hi Ajay,

Thanks for the test image. I checked it and found that Image-Pro does EDF on all time points only if the image set contains multiple channels. We will fix the problem in the next patch, so single-channel image sets will be processed as well.
As a workaround for the current version I've created a macro (attached) that will process all time points. 

1. Open the attached project from the Apps tab. (or Project Explorer)
2. Open one of the wells with all time points from your LIF file.
3. Run "EDFAllTimePoints" macro from EDFImageSet project - it will create a new image set with EDF projections of every time point. (e.g. 23 time points image set)
4. Repeat steps 2-3 for every image set in LIF file.

Best regards,

Yuri

YuriG

Hi Ajay,

Be sure you are using the latest version (10.0.7), it creates EDF for a complete set (all wells, all locations), the same for Maximum/Minimum functions (in case you need to create MIP image from Z-planes of every well).

Yuri

ajay_zalavadia

Yuri, I am running 10.0.7 Build 7018, 64-Bit
When I make EDF, I only end up having a single image at the active timepoint. Do i have to select all the timepoints ! and how ?

Attached here is LIF file content information:
each position has 23 timepoint and variable z-stacks.

YuriG

It looks like your LIF file contains multiple image sets, where every set is taken for a single well (with different number of Z position). I don't know if you can open them as a single multi-well, multi-Z image set (only in that case EDF will be created for all wells in one go). So the issue is not in EDF, but how these sets were acquired and can be opened in Image-Pro.

Yuri

ajay_zalavadia

Yuri, you are correct. this experiment does not have any information about the well.

This is one the common setup we use when dealing with 6-well plates. Most of the time we do not intend to image the whole well so instead we use Mark and Find setup in Leica LAS-X. This setup lets' let us pick positions around entire well plate irrespective of the well. We pick multiple positions and setup a time lapse for experiments such as cell motility assay or wound healing assay. The image pro is able to recognize the file just as it should be.

If i open each position one by one is it possible to have a macro/script that makes EDF at each time point and store the resulting EDFs as time series ? I can then manually open each position and apply the macro/script.

I tried recording macro on one of the position make EDF and clicking next on the time navigation at the bottom of the viewer. When I looked at the macro it recorded the hardwired  index numbers referring to each time point. I haven't had any luck with getting the number of time points from the open data set and looping through to make EDFs. You may have a better idea.

YuriG

Ajay,

If your image set is opened as a multi-Z, Time series, then all time points supposed to be processed by EDF in one operation.
If it's not the case, can you please send me a representative test image, so I can look at it? 

Click here to upload files.

Thanks,

Yuri

ajay_zalavadia

Yuri, the original file was 46GB. I removed all the other positions except first two, and still left with 2.1GB LIF file that I am uploading for you to test with. I am uploading Organoids-Testfile.lif in the background as I type this msg, will check on the progress tomorrow.

Ajay

ajay_zalavadia

Yuri, thank you. I was able to use the function you provided to make EDFs at each timepoint. That worked well. How do I export the resulting time series as multipage TIFF (time series) ?

YuriG

Hi Ajay,

You can click the Extract dimension button

and then save the result sequence as TIF (or in any other multi-frame format).

Yuri

ajay_zalavadia

Thank you.