Open Microscopy Environment

Hello,

We are running CellSens on our Olympus and collecting 3-d time-lapse. So far, one channel, multiple z-slices, and multiple time-points. When I import the .vsi file into Fiji, it only shows one single time-point. The series option box shows only 38 planes (we had 38 z-planes). This is in contrast to when we open Volocity .mvd files. With the .mvd file, I do get import of all timepoints, and the series option box shows the total sum of all planes (time x channels x z-sections).

Does anyone know if there are any solutions to this problem, or if I am just doing something wrong?

If not, are there any reasonable & temporary workarounds? Such as using CellSens to export TIFF series, or something to that effect?

Thanks for any advice on this helpful message board.

Please feel free to email me with any feedback as well.

Jake Hines
Biology Dept.
Winona State University
jhhines (at) winona.edu

Dear Jake,

thanks for your report and sorry to hear about your issues with CellSens files.
First of all, can you confirm the version of Bio-Formats you are using Fiji is updated to the latest release? If the problem is confirmed with Bio-Format 5.1.4, would it be possible for you to upload a sample vsi file
at http://qa.openmicroscopy.org.uk/qa/upload/?

Best regards,
Sebastien

Sebastian,

Thank you very much. I updated Fiji and as far as I can tell, we are running BioFormats version = 3 September 2015. Fiji app 5.1.4.jar

I have uploaded .vsi file and the corresponding .ets file, which is normally rooted in folders "_f1 lateral 25hpf yen4 20x timelapse_" and sub-folder "stack1"

I greatly appreciate your effort.

Best regards,
Jake

Hi Jake,

Thank you for submitting your files.
We were able to reproduce the issue locally.

I have created a ticket on this regard,
https://trac.openmicroscopy.org/ome/ticket/13029
We can also add you to the cc list, if you could give us your email id.

In the mean time,please follow the ticket to get notified on status changes.

Best,
Balaji

Hi Balaji,
We greatly appreciate your time. My email address is jhhines@winona.edu
All the best,
Jake

Hello,
Several months have passed and I wanted to follow up to see if any progress has been made on enabling 3-d time-lapse viewing in CellSens vsi files.
Thanks,
Jake Hines

Hi,

The fix for the issue should most probably get included in the next major release of Bio-Formats (5.2.0).This should happen later this spring.
We will keep you notified via the ticket, if this changes.

Best,
Balaji

Thank you very much. We appreciate your time to work on this!