How do you store original raw data as saved from the microscopes?

[emartini (Emanuele Martini)]

Dear all,
sorry for jump in this thread after one year.
But we are now in our institute do some Proof-Of-Concept and tests of Omero for the whole campus, and we are now reaching this question: why there is not a sub-folders structure.
I understood the point and reasons.
I’ve just a question: how do you store original raw data as saved from the microscopes?
Just for an example the .vsi produced by olympus is something like this:

Do you “destroy” the original structure organization of raw data?
How do you import this kind of experiment?

Thanks,
Emanuele

[joshmoore]

Hi @emartini,

I don’t think I full understand your question. Are you wondering where the previous structure was in the clients, i.e. in the UI for users? Or in the backend server? Can you show us a screenshot of where the structure has gone missing?

If you’re asking about the UI, then OMERO doesn’t expose the complexity of the file inputs to users but shows them the best representation of the image data itself.

If you’re asking about the backend, OMERO copies the hierarchy of files as detected by Bio-Formats to a subdirectory of /OMERO/ManagedRepository. If there are files that are not recognized by Bio-Formats, they won’t be copied.

Sorry if I’m misunderstanding.
~Josh

[emartini (Emanuele Martini)]

Ok, yes let me try to explain myself better.

I’ve now tried to import this experiment (the main folder itself, how the microscope saves it) using OMERO.insight this way:

The result on my OMERO.web is this:

so, it seems to me that I am losing the raw data folder organization and also a little bit of understanding of who is who.

For example, it will be a little bit tricky to understand if the image I’ve selected (10_cfDAPI_01.vsi) is the DAPI image of the 10th field of condition 1 or condition 2 (as they were in the organization of the folders here )

Will I have to put all the metadata and K-V pairs to subdivide them in conditions, field etc?
And there are many other data structures saving from all the other microscopes, for all of them we will have to invent a script or a way to automatically upload’em with the appropriate K-V pair and metadata?

I am just wondering if it will be suitable for all of our use cases in an Imaging Facility.

And then if someone will ask us to give them the original data as saved from the microscopes, Will I be able to retrieve them exactly as they were saved including their folder structure? Or Must I keep also the original data coming from the microscope?

[emartini (Emanuele Martini)]

for example, outside omero if I want to open the 3channels of the 3rd field of condition 1, I will go here:

[Sylvielg (Sylvie Le Guyader)]

Hi Emanuele

As I understood from the latest Omero user meeting, there are tools (autotagger plugin) that can automatically tag your data with the names of the folders they are in (imported path encrypted in the metadata). So the folder structure can be searched for keywords. Tagging as many advantages over nested folders.

However I think that there are still an issue that somehow stops me to fully implement Omero at our facility. As I understood there are 2 main ways to import data:

• In-place import which saves a hard link to the data location. This only works if nothing is changed to the storage: no moving, deleting or renaming files. However the images can be tagged and moved around in the database. So one should turn the database into a Read only folder to avoid broken links in the database. The advantage is that the data stays in the original format and it is not duplicated. I got the impression that this option is not totally easy to implement. I also got the impression that one cannot have the data on different servers or something like that.
• The other way is to use Omero import. The data and metadata is save to the database as OME TIFF. One can download the data and metadata in that format later. The advantage is that if one deletes or renames files, this will nicely be reflected in the database. Then one has 2 choices, either keeping or deleting the original files after upload. The first option leads to a duplication of the data which is obviously far from ideal but one could potentially go back to the file in the original format, open it on the microscope and press the Reuse button to reuse all the settings. In the second option, one loses the possibility to hit the Reuse button but one can still look at the metadata and set everything manually in the same way on the microscope. Less user friendly and slightly scary to delete the data in the original format after telling users for years to never ever delete the original data…

I’d love to hear from the Omero people if I misunderstood/forgot something.

[s.besson (Sébastien Besson)]

Hi Sylvie, thanks for chiming in and mentioning the autotag plugin (https://pypi.org/project/omero-webtagging-autotag/) developed by the Micron Imaging facility and provides a way to convert the original folder structure into searchable tags.

One quick clarification about the following:

The other way is to use Omero import. The data and metadata is save to the database as OME TIFF.

This is unfortunately a classical misundertanding which never happened for any version of OMERO.
In OMERO 4, the data import converted the original data into an internal representation which is not OME-TIFF.
In OMERO 5, the import process kept the data in its original file format, reads it via Bio-Formats at runtime. Imported images can then either be downloaded in their original format or exported using an exchangeable file format like OME-TIFF.

[Sylvielg (Sylvie Le Guyader)]

Hi Sébastien

Cool! Then I completely misunderstood! That puts Omero back on my work desk.

So the question left is how do we convince people who have tons of data in nested folders like Emanuele to swiftly move everything to Omero and delete their original folder structure?

Do I then understand correctly that Key Value are better for sorting than tags but that the tagging tool turns folders into tags and not into Key Values?

I have the exact same problem as Emanuele:

• If we upload images in nested folders with the tagging tool, how easy is it to retrieve the images of a given condition that was described in the folder names
• When the users leaves the facility and wants to export their data, how can the user find their way without an Omero server?

[emartini (Emanuele Martini)]

@Sylvielg

is how do we convince people who have tons of data in nested folders like Emanuele

just an add many times it is not the user who saves nested folders
it is the microscope itself.

[emartini (Emanuele Martini)]

@joshmoore

If you’re asking about the backend, OMERO copies the hierarchy of files as detected by Bio-Formats to a subdirectory of /OMERO/ManagedRepository

thisi is what I see in ManagedRepository

I’ve some problem to find the hierarchy of files, and even the name of the experiment itself.
Inside a folder called: 07-13-23.704 there is this .tif file:

of course in my original folder, there is no folder called: 07-13-23.704

On a side note,

@joshmoore

If there are files that are not recognized by Bio-Formats, they won’t be copied.

this in general could be a problem if we would like to use omero as storage of raw data from the microscope.
If a microscope will save some files not recognized by bioformats, we will need an extra copy on another server of the raw data as saved by the microscope.

[emartini (Emanuele Martini)]

For example, if I search for this file 8_cfDAPI_01.vsi in the OMERO/ManagedRepository/
I will find that:

Which of these is this file of my experiment raw data?

About the other issue, the one related to not recognized files by bioformats, this Olympus microscope saves also a .oex file.

it’s not present in the Omero/ManagedRepository

sorry for bothering you with all these questions and doubts, but we are now pushing to test omero for our institute so we will have a lot of questions…

[joshmoore]

@emartini

I’ve some problem to find the hierarchy of files, and even the name of the experiment itself.
Inside a folder called: 07-13-23.704 there is this .tif file:

This says to me that your dataset isn’t being detected as a Bio-Formats format but rather just as a collection of TIFFs.

@emartini

of course in my original folder, there is no folder called: 07-13-23.704

That meets my expectation. Everything up to the timestamped directory is created by the server for management purposes. What’s below matches what Bio-Formats can detect from your experiment.

@emartini

sorry for bothering you with all these questions and doubts, but we are now pushing to test omero for our institute so we will have a lot of questions…

No worries! That’s what we’re here for.
~J.

[emartini (Emanuele Martini)]

We will try in the next days to upload not touched images and files(no folder rename, no file rename, no extra files, no analysis performed on them): just as they come out from the microscope, and see how they’ll be uploaded in omero (web and server).

We are a little bit worried that we must keep a server with the raw data and just use omero as a viewer and not really a db for raw data.

[joshmoore]

Sounds good, @emartini. Keep us posted. Do note that you can also use Bio-Formats or even omero import -f locally to get a feel for how a folder will be uploaded if that will simplify your investigations.

All the best,
~Josh

[emartini (Emanuele Martini)]

thank you for the suggestion,
we will also explore in-place import for sure
https://docs.openmicroscopy.org/omero/5.6.2/sysadmins/in-place-import.html

[emartini (Emanuele Martini)]

Dear All,
we have tried to import this experiment acquired at CSU Olympus microscope.
These FRAP acquisitions are organized like that:
2 conditions
different field time lapse
folder with roi where we performed the laser FRAP

This is the tree via command line of the original folder from the microscope:

Z:.
▒▒▒▒SiCDK12_2
▒   ▒   Experiment.oex
▒   ▒
▒   ▒▒▒▒Folder01
▒   ▒       Image_01.tif
▒   ▒
▒   ▒▒▒▒Folder02
▒   ▒       Image_02.tif
▒   ▒
▒   ▒▒▒▒Folder03
▒   ▒       Image_03.tif
▒   ▒
▒   ▒▒▒▒Folder04
▒   ▒       Image_04.tif
▒   ▒
▒   ▒▒▒▒Folder05
▒   ▒       Image_05.tif
▒   ▒
▒   ▒▒▒▒Folder06
▒   ▒       Image_06.tif
▒   ▒
▒   ▒▒▒▒Folder07
▒   ▒       Image_07.tif
▒   ▒
▒   ▒▒▒▒Folder08
▒   ▒       Image_08.tif
▒   ▒
▒   ▒▒▒▒Folder09
▒   ▒       Image_09.tif
▒   ▒
▒   ▒▒▒▒Folder10
▒   ▒       Image_10.tif
▒   ▒
▒   ▒▒▒▒Folder11
▒   ▒       Image_11.tif
▒   ▒
▒   ▒▒▒▒Folder12
▒   ▒       Image_12.tif
▒   ▒
▒   ▒▒▒▒Folder13
▒   ▒       Image_13.tif
▒   ▒
▒   ▒▒▒▒Folder14
▒   ▒       Image_14.tif
▒   ▒
▒   ▒▒▒▒Folder15
▒   ▒       Image_15.tif
▒   ▒
▒   ▒▒▒▒Folder16
▒   ▒       Image_16.tif
▒   ▒
▒   ▒▒▒▒Folder17
▒   ▒       Image_17.tif
▒   ▒
▒   ▒▒▒▒Folder18
▒   ▒       Image_18.tif
▒   ▒
▒   ▒▒▒▒Folder19
▒   ▒       Image_19.tif
▒   ▒
▒   ▒▒▒▒Folder20
▒   ▒       Image_20.tif
▒   ▒
▒   ▒▒▒▒Folder21
▒   ▒       Image_21.tif
▒   ▒
▒   ▒▒▒▒Folder22
▒   ▒       Image_22.tif
▒   ▒
▒   ▒▒▒▒Folder23
▒   ▒       Image_23.tif
▒   ▒
▒   ▒▒▒▒Folder24
▒   ▒       Image_24.tif
▒   ▒
▒   ▒▒▒▒Folder_01cfFITC
▒   ▒   ▒   current_cfFITC_01.oex
▒   ▒   ▒   current_cfFITC_01.vsi
▒   ▒   ▒   Image_01.tif
▒   ▒   ▒
▒   ▒   ▒▒▒▒_current_cfFITC_01_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
▒   ▒
▒   ▒▒▒▒Folder_02cfFITC
▒   ▒   ▒   current_cfFITC_02.oex
▒   ▒   ▒   current_cfFITC_02.vsi
▒   ▒   ▒   Image_02.tif
▒   ▒   ▒
▒   ▒   ▒▒▒▒_current_cfFITC_02_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
▒   ▒
▒   ▒▒▒▒Folder_03cfFITC
▒   ▒   ▒   current_cfFITC_03.oex
▒   ▒   ▒   current_cfFITC_03.vsi
▒   ▒   ▒   Image_03.tif
▒   ▒   ▒
▒   ▒   ▒▒▒▒_current_cfFITC_03_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
▒   ▒
▒   ▒▒▒▒Folder_04cfFITC
▒   ▒   ▒   current_cfFITC_04.oex
▒   ▒   ▒   current_cfFITC_04.vsi
▒   ▒   ▒   Image_04.tif
▒   ▒   ▒
▒   ▒   ▒▒▒▒_current_cfFITC_04_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
▒   ▒
▒   ▒▒▒▒Folder_05cfFITC
▒   ▒   ▒   current_cfFITC_05.oex
▒   ▒   ▒   current_cfFITC_05.vsi
▒   ▒   ▒   Image_05.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_05_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
▒   ▒
▒   ▒▒▒▒Folder_06cfFITC
▒   ▒   ▒   current_cfFITC_06.oex
▒   ▒   ▒   current_cfFITC_06.vsi
▒   ▒   ▒   Image_06.tif
▒   ▒   ▒
▒   ▒   ▒▒▒▒_current_cfFITC_06_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
▒   ▒
▒   ▒▒▒▒Folder_07cfFITC
▒   ▒   ▒   current_cfFITC_07.oex
▒   ▒   ▒   current_cfFITC_07.vsi
▒   ▒   ▒   Image_07.tif
▒   ▒   ▒
▒   ▒   ▒▒▒▒_current_cfFITC_07_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
▒   ▒
▒   ▒▒▒▒Folder_08cfFITC
▒   ▒   ▒   current_cfFITC_08.oex
▒   ▒   ▒   current_cfFITC_08.vsi
▒   ▒   ▒   Image_08.tif
▒   ▒   ▒
▒   ▒   ▒▒▒▒_current_cfFITC_08_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
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▒   ▒▒▒▒Folder_09cfFITC
▒   ▒   ▒   current_cfFITC_09.oex
▒   ▒   ▒   current_cfFITC_09.vsi
▒   ▒   ▒   Image_09.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_09_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
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▒   ▒▒▒▒Folder_10cfFITC
▒   ▒   ▒   current_cfFITC_10.oex
▒   ▒   ▒   current_cfFITC_10.vsi
▒   ▒   ▒   Image_10.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_10_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
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▒   ▒▒▒▒Folder_11cfFITC
▒   ▒   ▒   current_cfFITC_11.oex
▒   ▒   ▒   current_cfFITC_11.vsi
▒   ▒   ▒   Image_11.tif
▒   ▒   ▒
▒   ▒   ▒▒▒▒_current_cfFITC_11_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
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▒   ▒▒▒▒Folder_12cfFITC
▒   ▒   ▒   current_cfFITC_12.oex
▒   ▒   ▒   current_cfFITC_12.vsi
▒   ▒   ▒   Image_12.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_12_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
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▒   ▒▒▒▒Folder_13cfFITC
▒   ▒   ▒   current_cfFITC_13.oex
▒   ▒   ▒   current_cfFITC_13.vsi
▒   ▒   ▒   Image_13.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_13_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
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▒   ▒▒▒▒Folder_14cfFITC
▒   ▒   ▒   current_cfFITC_14.oex
▒   ▒   ▒   current_cfFITC_14.vsi
▒   ▒   ▒   Image_14.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_14_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
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▒   ▒▒▒▒Folder_15cfFITC
▒   ▒   ▒   current_cfFITC_15.oex
▒   ▒   ▒   current_cfFITC_15.vsi
▒   ▒   ▒   Image_15.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_15_
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▒   ▒▒▒▒Folder_16cfFITC
▒   ▒   ▒   current_cfFITC_16.oex
▒   ▒   ▒   current_cfFITC_16.vsi
▒   ▒   ▒   Image_16.tif
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▒   ▒▒▒▒Folder_17cfFITC
▒   ▒   ▒   current_cfFITC_17.oex
▒   ▒   ▒   current_cfFITC_17.vsi
▒   ▒   ▒   Image_17.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_17_
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▒   ▒▒▒▒Folder_18cfFITC
▒   ▒   ▒   current_cfFITC_18.oex
▒   ▒   ▒   current_cfFITC_18.vsi
▒   ▒   ▒   Image_18.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_18_
▒   ▒       ▒▒▒▒stack1
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▒   ▒▒▒▒Folder_19cfFITC
▒   ▒   ▒   current_cfFITC_19.oex
▒   ▒   ▒   current_cfFITC_19.vsi
▒   ▒   ▒   Image_19.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_19_
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▒   ▒▒▒▒Folder_20cfFITC
▒   ▒   ▒   current_cfFITC_20.oex
▒   ▒   ▒   current_cfFITC_20.vsi
▒   ▒   ▒   Image_20.tif
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▒   ▒   ▒▒▒▒_current_cfFITC_20_
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▒   ▒▒▒▒Folder_21cfFITC
▒   ▒   ▒   current_cfFITC_21.oex
▒   ▒   ▒   current_cfFITC_21.vsi
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▒   ▒▒▒▒Folder_22cfFITC
▒   ▒   ▒   current_cfFITC_22.oex
▒   ▒   ▒   current_cfFITC_22.vsi
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▒   ▒   ▒   current_cfFITC_24.oex
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▒   ▒   ▒▒▒▒_current_cfFITC_24_
▒   ▒       ▒▒▒▒stack1
▒   ▒               frame_t_0.ets
▒   ▒
▒   ▒▒▒▒ROI
▒   ▒       Image_01.tif
▒   ▒       Image_02.tif
▒   ▒       Image_03.tif
▒   ▒       Image_04.tif
▒   ▒       Image_05.tif
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▒   ▒       Image_24.tif
▒   ▒
▒   ▒▒▒▒_temp
▒▒▒▒SiRLUC
    ▒   Experiment.oex
    ▒
    ▒▒▒▒Folder01
    ▒       Image_01.tif
    ▒
    ▒▒▒▒Folder02
    ▒       Image_02.tif
    ▒
    ▒▒▒▒Folder03
    ▒       Image_03.tif
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    ▒       Image_04.tif
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    ▒       Image_05.tif
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    ▒       Image_06.tif
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    ▒▒▒▒Folder07
    ▒       Image_07.tif
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    ▒▒▒▒Folder08
    ▒       Image_08.tif
    ▒
    ▒▒▒▒Folder09
    ▒       Image_09.tif
    ▒
    ▒▒▒▒Folder10
    ▒       Image_10.tif
    ▒
    ▒▒▒▒Folder11
    ▒       Image_11.tif
    ▒
    ▒▒▒▒Folder12
    ▒       Image_12.tif
    ▒
    ▒▒▒▒Folder13
    ▒       Image_13.tif
    ▒
    ▒▒▒▒Folder14
    ▒       Image_14.tif
    ▒
    ▒▒▒▒Folder_01cfFITC
    ▒   ▒   current_cfFITC_01.oex
    ▒   ▒   current_cfFITC_01.vsi
    ▒   ▒   Image_01.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_01_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_02cfFITC
    ▒   ▒   current_cfFITC_02.oex
    ▒   ▒   current_cfFITC_02.vsi
    ▒   ▒   Image_02.tif
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    ▒
    ▒▒▒▒Folder_03cfFITC
    ▒   ▒   current_cfFITC_03.oex
    ▒   ▒   current_cfFITC_03.vsi
    ▒   ▒   Image_03.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_03_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_04cfFITC
    ▒   ▒   current_cfFITC_04.oex
    ▒   ▒   current_cfFITC_04.vsi
    ▒   ▒   Image_04.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_04_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_05cfFITC
    ▒   ▒   current_cfFITC_05.oex
    ▒   ▒   current_cfFITC_05.vsi
    ▒   ▒   Image_05.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_05_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_06cfFITC
    ▒   ▒   current_cfFITC_06.oex
    ▒   ▒   current_cfFITC_06.vsi
    ▒   ▒   Image_06.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_06_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_07cfFITC
    ▒   ▒   current_cfFITC_07.oex
    ▒   ▒   current_cfFITC_07.vsi
    ▒   ▒   Image_07.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_07_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_08cfFITC
    ▒   ▒   current_cfFITC_08.oex
    ▒   ▒   current_cfFITC_08.vsi
    ▒   ▒   Image_08.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_08_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_09cfFITC
    ▒   ▒   current_cfFITC_09.oex
    ▒   ▒   current_cfFITC_09.vsi
    ▒   ▒   Image_09.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_09_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_10cfFITC
    ▒   ▒   current_cfFITC_10.oex
    ▒   ▒   current_cfFITC_10.vsi
    ▒   ▒   Image_10.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_10_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_11cfFITC
    ▒   ▒   current_cfFITC_11.oex
    ▒   ▒   current_cfFITC_11.vsi
    ▒   ▒   Image_11.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_11_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_12cfFITC
    ▒   ▒   current_cfFITC_12.oex
    ▒   ▒   current_cfFITC_12.vsi
    ▒   ▒   Image_12.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_12_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_13cfFITC
    ▒   ▒   current_cfFITC_13.oex
    ▒   ▒   current_cfFITC_13.vsi
    ▒   ▒   Image_13.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_13_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒Folder_14cfFITC
    ▒   ▒   current_cfFITC_14.oex
    ▒   ▒   current_cfFITC_14.vsi
    ▒   ▒   Image_14.tif
    ▒   ▒
    ▒   ▒▒▒▒_current_cfFITC_14_
    ▒       ▒▒▒▒stack1
    ▒               frame_t_0.ets
    ▒
    ▒▒▒▒ROI
    ▒       Image_01.tif
    ▒       Image_02.tif
    ▒       Image_03.tif
    ▒       Image_04.tif
    ▒       Image_05.tif
    ▒       Image_06.tif
    ▒       Image_07.tif
    ▒       Image_08.tif
    ▒       Image_09.tif
    ▒       Image_10.tif
    ▒       Image_11.tif
    ▒       Image_12.tif
    ▒       Image_13.tif
    ▒       Image_14.tif
    ▒
    ▒▒▒▒_temp
            ois121F.info
            ois121F.vsi

Maybe clearer with a screenshot:
Time Lapse folders .vsi and .ets files in the named Folder_0x

Then the scientist wanted to have one folder for each field with the snapshot of the field in the named Folder0x
And another folder called ROI where you can see the area selected for the FRAP.
for both of the two conditions condition.

If you see the tree it’s complicated but at the end of the day it’s clear:

1. first folder: name of the condition
2. subfolders Folder_0x with the underscore: the timelapse of a field of that condition
3. subfolders Folder0x without an underscore: the snapshot of a field analyzed of that condition
4. subfolders called ROI: with the ROI overlaid where FRAP was performed.

I imported it in OMERO, this is what this scientist will see:

The same for the other condition.

So, in my opinion, it will be very uncomfy for the scientist to browse this experiment using a simple way to import via omero.insight.
But serving around 100 users with different kinds of experiments, microscopes, file formats, experiment types… it would be nice to have a simple way to import data.

[emartini (Emanuele Martini)]

---

Let’s pass to the server-side OMERO/ManagedRepository.
First of all, I’ve to found it remembering the date when I imported it.
It’s imported like that:

.
├── ./11-36-26.108
│   └── ./11-36-26.108/Image_08.tif
├── ./11-36-26.108.log
├── ./11-36-26.948
│   └── ./11-36-26.948/Image_20.tif
├── ./11-36-26.948.log
├── ./11-36-28.060
│   ├── ./11-36-28.060/_current_cfFITC_16_
│   │   └── ./11-36-28.060/_current_cfFITC_16_/stack1
│   │       └── ./11-36-28.060/_current_cfFITC_16_/stack1/frame_t_0.ets
│   └── ./11-36-28.060/current_cfFITC_16.vsi
├── ./11-36-28.060.log
├── ./11-36-44.485
│   ├── ./11-36-44.485/_current_cfFITC_04_
│   │   └── ./11-36-44.485/_current_cfFITC_04_/stack1
│   │       └── ./11-36-44.485/_current_cfFITC_04_/stack1/frame_t_0.ets
│   └── ./11-36-44.485/current_cfFITC_04.vsi
├── ./11-36-44.485.log
├── ./11-36-58.292
│   ├── ./11-36-58.292/_current_cfFITC_20_
│   │   └── ./11-36-58.292/_current_cfFITC_20_/stack1
│   │       └── ./11-36-58.292/_current_cfFITC_20_/stack1/frame_t_0.ets
│   └── ./11-36-58.292/current_cfFITC_20.vsi
├── ./11-36-58.292.log
├── ./11-37-12.328
│   └── ./11-37-12.328/Image_13.tif
├── ./11-37-12.328.log
├── ./11-37-12.986
│   └── ./11-37-12.986/Image_03.tif
├── ./11-37-12.986.log
├── ./11-37-13.644
│   └── ./11-37-13.644/Image_20.tif
├── ./11-37-13.644.log
├── ./11-37-14.294
│   └── ./11-37-14.294/Image_14.tif
├── ./11-37-14.294.log
├── ./11-37-15.172
│   └── ./11-37-15.172/Image_11.tif
├── ./11-37-15.172.log
├── ./11-37-15.781
│   └── ./11-37-15.781/Image_22.tif
├── ./11-37-15.781.log
├── ./11-37-16.435
│   ├── ./11-37-16.435/_current_cfFITC_23_
│   │   └── ./11-37-16.435/_current_cfFITC_23_/stack1
│   │       └── ./11-37-16.435/_current_cfFITC_23_/stack1/frame_t_0.ets
│   └── ./11-37-16.435/current_cfFITC_23.vsi
├── ./11-37-16.435.log
├── ./11-37-30.550
│   ├── ./11-37-30.550/_current_cfFITC_01_
│   │   └── ./11-37-30.550/_current_cfFITC_01_/stack1
│   │       └── ./11-37-30.550/_current_cfFITC_01_/stack1/frame_t_0.ets
│   └── ./11-37-30.550/current_cfFITC_01.vsi
├── ./11-37-30.550.log
├── ./11-37-44.302
│   ├── ./11-37-44.302/_current_cfFITC_09_
│   │   └── ./11-37-44.302/_current_cfFITC_09_/stack1
│   │       └── ./11-37-44.302/_current_cfFITC_09_/stack1/frame_t_0.ets
│   └── ./11-37-44.302/current_cfFITC_09.vsi
├── ./11-37-44.302.log
├── ./11-37-58.134
│   └── ./11-37-58.134/Image_03.tif
├── ./11-37-58.134.log
├── ./11-37-58.811
│   ├── ./11-37-58.811/_current_cfFITC_01_
│   │   └── ./11-37-58.811/_current_cfFITC_01_/stack1
│   │       └── ./11-37-58.811/_current_cfFITC_01_/stack1/frame_t_0.ets
│   └── ./11-37-58.811/current_cfFITC_01.vsi
├── ./11-37-58.811.log
├── ./11-38-12.845
│   ├── ./11-38-12.845/_current_cfFITC_07_
│   │   └── ./11-38-12.845/_current_cfFITC_07_/stack1
│   │       └── ./11-38-12.845/_current_cfFITC_07_/stack1/frame_t_0.ets
│   └── ./11-38-12.845/current_cfFITC_07.vsi
├── ./11-38-12.845.log
├── ./11-38-26.139
│   └── ./11-38-26.139/Image_14.tif
├── ./11-38-26.139.log
├── ./11-38-26.656
│   └── ./11-38-26.656/Image_08.tif
├── ./11-38-26.656.log
├── ./11-38-27.227
│   └── ./11-38-27.227/Image_03.tif
├── ./11-38-27.227.log
├── ./11-38-27.775
│   └── ./11-38-27.775/Image_04.tif
├── ./11-38-27.775.log
├── ./11-38-28.541
│   └── ./11-38-28.541/Image_09.tif
├── ./11-38-28.541.log
├── ./11-38-29.208
│   └── ./11-38-29.208/Image_03.tif
├── ./11-38-29.208.log
├── ./11-38-29.839
│   └── ./11-38-29.839/Image_14.tif
├── ./11-38-29.839.log
├── ./11-38-30.421
│   └── ./11-38-30.421/Image_04.tif
├── ./11-38-30.421.log
├── ./11-38-31.078
│   ├── ./11-38-31.078/_current_cfFITC_06_
│   │   └── ./11-38-31.078/_current_cfFITC_06_/stack1
│   │       └── ./11-38-31.078/_current_cfFITC_06_/stack1/frame_t_0.ets
│   └── ./11-38-31.078/current_cfFITC_06.vsi
├── ./11-38-31.078.log
├── ./11-38-44.994
│   ├── ./11-38-44.994/_current_cfFITC_10_
│   │   └── ./11-38-44.994/_current_cfFITC_10_/stack1
│   │       └── ./11-38-44.994/_current_cfFITC_10_/stack1/frame_t_0.ets
│   └── ./11-38-44.994/current_cfFITC_10.vsi
├── ./11-38-44.994.log
├── ./11-38-58.470
│   └── ./11-38-58.470/Image_08.tif
├── ./11-38-58.470.log
├── ./11-38-58.961
│   └── ./11-38-58.961/Image_05.tif
├── ./11-38-58.961.log
├── ./11-38-59.511
│   └── ./11-38-59.511/Image_19.tif
├── ./11-38-59.511.log
├── ./11-39-00.115
│   └── ./11-39-00.115/Image_17.tif
├── ./11-39-00.115.log
├── ./11-39-00.679
│   └── ./11-39-00.679/Image_08.tif
├── ./11-39-00.679.log
├── ./11-39-01.239
│   └── ./11-39-01.239/Image_16.tif
├── ./11-39-01.239.log
├── ./11-39-02.043
│   └── ./11-39-02.043/Image_12.tif
├── ./11-39-02.043.log
├── ./11-39-02.835
│   ├── ./11-39-02.835/_current_cfFITC_13_
│   │   └── ./11-39-02.835/_current_cfFITC_13_/stack1
│   │       └── ./11-39-02.835/_current_cfFITC_13_/stack1/frame_t_0.ets
│   └── ./11-39-02.835/current_cfFITC_13.vsi
├── ./11-39-02.835.log
├── ./11-39-17.207
│   └── ./11-39-17.207/Image_20.tif
├── ./11-39-17.207.log
├── ./11-39-17.709
│   └── ./11-39-17.709/Image_09.tif
├── ./11-39-17.709.log
├── ./11-39-18.267
│   └── ./11-39-18.267/Image_04.tif
├── ./11-39-18.267.log
├── ./11-39-18.915
│   ├── ./11-39-18.915/_current_cfFITC_11_
│   │   └── ./11-39-18.915/_current_cfFITC_11_/stack1
│   │       └── ./11-39-18.915/_current_cfFITC_11_/stack1/frame_t_0.ets
│   └── ./11-39-18.915/current_cfFITC_11.vsi
├── ./11-39-18.915.log
├── ./11-39-33.281
│   └── ./11-39-33.281/Image_16.tif
├── ./11-39-33.281.log
├── ./11-39-33.815
│   └── ./11-39-33.815/Image_09.tif
├── ./11-39-33.815.log
├── ./11-39-34.578
│   └── ./11-39-34.578/Image_02.tif
├── ./11-39-34.578.log
├── ./11-39-35.362
│   └── ./11-39-35.362/Image_10.tif
├── ./11-39-35.362.log
├── ./11-39-36.040
│   ├── ./11-39-36.040/_current_cfFITC_07_
│   │   └── ./11-39-36.040/_current_cfFITC_07_/stack1
│   │       └── ./11-39-36.040/_current_cfFITC_07_/stack1/frame_t_0.ets
│   └── ./11-39-36.040/current_cfFITC_07.vsi
├── ./11-39-36.040.log
├── ./11-39-49.837
│   ├── ./11-39-49.837/_current_cfFITC_18_
│   │   └── ./11-39-49.837/_current_cfFITC_18_/stack1
│   │       └── ./11-39-49.837/_current_cfFITC_18_/stack1/frame_t_0.ets
│   └── ./11-39-49.837/current_cfFITC_18.vsi
├── ./11-39-49.837.log
├── ./11-40-03.571
│   └── ./11-40-03.571/Image_07.tif
├── ./11-40-03.571.log
├── ./11-40-04.159
│   └── ./11-40-04.159/Image_08.tif
├── ./11-40-04.159.log
├── ./11-40-04.837
│   └── ./11-40-04.837/Image_24.tif
├── ./11-40-04.837.log
├── ./11-40-05.485
│   └── ./11-40-05.485/Image_01.tif
├── ./11-40-05.485.log
├── ./11-40-06.253
│   └── ./11-40-06.253/Image_02.tif
├── ./11-40-06.253.log
├── ./11-40-06.980
│   └── ./11-40-06.980/Image_13.tif
├── ./11-40-06.980.log
├── ./11-40-07.764
│   └── ./11-40-07.764/Image_07.tif
├── ./11-40-07.764.log
├── ./11-40-08.425
│   └── ./11-40-08.425/Image_18.tif
├── ./11-40-08.425.log
├── ./11-40-09.115
│   └── ./11-40-09.115/Image_24.tif
├── ./11-40-09.115.log
├── ./11-40-09.830
│   ├── ./11-40-09.830/_current_cfFITC_09_
│   │   └── ./11-40-09.830/_current_cfFITC_09_/stack1
│   │       └── ./11-40-09.830/_current_cfFITC_09_/stack1/frame_t_0.ets
│   └── ./11-40-09.830/current_cfFITC_09.vsi
├── ./11-40-09.830.log
├── ./11-40-23.632
│   └── ./11-40-23.632/Image_03.tif
├── ./11-40-23.632.log
├── ./11-40-24.329
│   └── ./11-40-24.329/Image_21.tif
├── ./11-40-24.329.log
├── ./11-40-25.128
│   ├── ./11-40-25.128/_current_cfFITC_21_
│   │   └── ./11-40-25.128/_current_cfFITC_21_/stack1
│   │       └── ./11-40-25.128/_current_cfFITC_21_/stack1/frame_t_0.ets
│   └── ./11-40-25.128/current_cfFITC_21.vsi
├── ./11-40-25.128.log
├── ./11-40-39.510
│   └── ./11-40-39.510/Image_02.tif
├── ./11-40-39.510.log
├── ./11-40-40.091
│   └── ./11-40-40.091/Image_10.tif
├── ./11-40-40.091.log
├── ./11-40-40.793
│   ├── ./11-40-40.793/_current_cfFITC_04_
│   │   └── ./11-40-40.793/_current_cfFITC_04_/stack1
│   │       └── ./11-40-40.793/_current_cfFITC_04_/stack1/frame_t_0.ets
│   └── ./11-40-40.793/current_cfFITC_04.vsi
├── ./11-40-40.793.log
├── ./11-40-54.817
│   ├── ./11-40-54.817/_current_cfFITC_15_
│   │   └── ./11-40-54.817/_current_cfFITC_15_/stack1
│   │       └── ./11-40-54.817/_current_cfFITC_15_/stack1/frame_t_0.ets
│   └── ./11-40-54.817/current_cfFITC_15.vsi
├── ./11-40-54.817.log
├── ./11-41-08.584
│   ├── ./11-41-08.584/_current_cfFITC_03_
│   │   └── ./11-41-08.584/_current_cfFITC_03_/stack1
│   │       └── ./11-41-08.584/_current_cfFITC_03_/stack1/frame_t_0.ets
│   └── ./11-41-08.584/current_cfFITC_03.vsi
├── ./11-41-08.584.log
├── ./11-41-22.401
│   ├── ./11-41-22.401/_current_cfFITC_14_
│   │   └── ./11-41-22.401/_current_cfFITC_14_/stack1
│   │       └── ./11-41-22.401/_current_cfFITC_14_/stack1/frame_t_0.ets
│   └── ./11-41-22.401/current_cfFITC_14.vsi
├── ./11-41-22.401.log
├── ./11-41-36.057
│   └── ./11-41-36.057/Image_23.tif
├── ./11-41-36.057.log
├── ./11-41-36.577
│   └── ./11-41-36.577/Image_09.tif
├── ./11-41-36.577.log
├── ./11-41-37.166
│   └── ./11-41-37.166/Image_13.tif
├── ./11-41-37.166.log
├── ./11-41-37.845
│   └── ./11-41-37.845/Image_04.tif
├── ./11-41-37.845.log
├── ./11-41-38.490
│   └── ./11-41-38.490/Image_12.tif
├── ./11-41-38.490.log
├── ./11-41-39.018
│   └── ./11-41-39.018/ois121F.vsi
├── ./11-41-39.018.log
├── ./11-41-39.617
│   └── ./11-41-39.617/Image_15.tif
├── ./11-41-39.617.log
├── ./11-41-40.181
│   └── ./11-41-40.181/Image_05.tif
├── ./11-41-40.181.log
├── ./11-41-40.766
│   └── ./11-41-40.766/Image_21.tif
├── ./11-41-40.766.log
├── ./11-41-41.431
│   └── ./11-41-41.431/Image_06.tif
├── ./11-41-41.431.log
├── ./11-41-42.095
│   └── ./11-41-42.095/Image_05.tif
├── ./11-41-42.095.log
├── ./11-41-42.957
│   ├── ./11-41-42.957/_current_cfFITC_06_
│   │   └── ./11-41-42.957/_current_cfFITC_06_/stack1
│   │       └── ./11-41-42.957/_current_cfFITC_06_/stack1/frame_t_0.ets
│   └── ./11-41-42.957/current_cfFITC_06.vsi
├── ./11-41-42.957.log
├── ./11-41-56.598
│   └── ./11-41-56.598/Image_19.tif
├── ./11-41-56.598.log
├── ./11-41-57.141
│   └── ./11-41-57.141/Image_06.tif
├── ./11-41-57.141.log
├── ./11-41-57.709
│   └── ./11-41-57.709/Image_22.tif
├── ./11-41-57.709.log
├── ./11-41-58.407
│   └── ./11-41-58.407/Image_23.tif
├── ./11-41-58.407.log
├── ./11-41-59.056
│   └── ./11-41-59.056/Image_02.tif
├── ./11-41-59.056.log
├── ./11-41-59.698
│   ├── ./11-41-59.698/_current_cfFITC_05_
│   │   └── ./11-41-59.698/_current_cfFITC_05_/stack1
│   │       └── ./11-41-59.698/_current_cfFITC_05_/stack1/frame_t_0.ets
│   └── ./11-41-59.698/current_cfFITC_05.vsi
├── ./11-41-59.698.log
├── ./11-42-13.202
│   └── ./11-42-13.202/Image_07.tif
├── ./11-42-13.202.log
├── ./11-42-13.691
│   └── ./11-42-13.691/Image_06.tif
├── ./11-42-13.691.log
├── ./11-42-14.232
│   └── ./11-42-14.232/Image_14.tif
├── ./11-42-14.232.log
├── ./11-42-14.799
│   └── ./11-42-14.799/Image_07.tif
├── ./11-42-14.799.log
├── ./11-42-15.469
│   └── ./11-42-15.469/Image_06.tif
├── ./11-42-15.469.log
├── ./11-42-16.128
│   └── ./11-42-16.128/Image_02.tif
├── ./11-42-16.128.log
├── ./11-42-16.734
│   └── ./11-42-16.734/Image_17.tif
├── ./11-42-16.734.log
├── ./11-42-17.429
│   └── ./11-42-17.429/Image_01.tif
├── ./11-42-17.429.log
├── ./11-42-17.993
│   ├── ./11-42-17.993/_current_cfFITC_12_
│   │   └── ./11-42-17.993/_current_cfFITC_12_/stack1
│   │       └── ./11-42-17.993/_current_cfFITC_12_/stack1/frame_t_0.ets
│   └── ./11-42-17.993/current_cfFITC_12.vsi
├── ./11-42-17.993.log
├── ./11-42-31.783
│   ├── ./11-42-31.783/_current_cfFITC_12_
│   │   └── ./11-42-31.783/_current_cfFITC_12_/stack1
│   │       └── ./11-42-31.783/_current_cfFITC_12_/stack1/frame_t_0.ets
│   └── ./11-42-31.783/current_cfFITC_12.vsi
├── ./11-42-31.783.log
├── ./11-42-45.059
│   └── ./11-42-45.059/Image_05.tif
├── ./11-42-45.059.log
├── ./11-42-45.589
│   └── ./11-42-45.589/Image_13.tif
├── ./11-42-45.589.log
├── ./11-42-46.205
│   └── ./11-42-46.205/Image_10.tif
├── ./11-42-46.205.log
├── ./11-42-46.922
│   └── ./11-42-46.922/Image_12.tif
├── ./11-42-46.922.log
├── ./11-42-47.500
│   └── ./11-42-47.500/Image_19.tif
├── ./11-42-47.500.log
├── ./11-42-48.092
│   └── ./11-42-48.092/Image_17.tif
├── ./11-42-48.092.log
├── ./11-42-48.660
│   └── ./11-42-48.660/Image_05.tif
├── ./11-42-48.660.log
├── ./11-42-49.354
│   ├── ./11-42-49.354/_current_cfFITC_17_
│   │   └── ./11-42-49.354/_current_cfFITC_17_/stack1
│   │       └── ./11-42-49.354/_current_cfFITC_17_/stack1/frame_t_0.ets
│   └── ./11-42-49.354/current_cfFITC_17.vsi
├── ./11-42-49.354.log
├── ./11-43-03.014
│   └── ./11-43-03.014/Image_09.tif
├── ./11-43-03.014.log
├── ./11-43-03.584
│   ├── ./11-43-03.584/_current_cfFITC_05_
│   │   └── ./11-43-03.584/_current_cfFITC_05_/stack1
│   │       └── ./11-43-03.584/_current_cfFITC_05_/stack1/frame_t_0.ets
│   └── ./11-43-03.584/current_cfFITC_05.vsi
├── ./11-43-03.584.log
├── ./11-43-17.016
│   └── ./11-43-17.016/Image_11.tif
├── ./11-43-17.016.log
├── ./11-43-17.564
│   └── ./11-43-17.564/Image_21.tif
├── ./11-43-17.564.log
├── ./11-43-18.456
│   └── ./11-43-18.456/Image_04.tif
├── ./11-43-18.456.log
├── ./11-43-18.974
│   └── ./11-43-18.974/Image_22.tif
├── ./11-43-18.974.log
├── ./11-43-19.522
│   └── ./11-43-19.522/Image_06.tif
├── ./11-43-19.522.log
├── ./11-43-20.036
│   └── ./11-43-20.036/Image_11.tif
├── ./11-43-20.036.log
├── ./11-43-20.550
│   └── ./11-43-20.550/Image_11.tif
├── ./11-43-20.550.log
├── ./11-43-21.141
│   └── ./11-43-21.141/Image_15.tif
├── ./11-43-21.141.log
├── ./11-43-21.735
│   └── ./11-43-21.735/Image_03.tif
├── ./11-43-21.735.log
├── ./11-43-22.333
│   └── ./11-43-22.333/Image_06.tif
├── ./11-43-22.333.log
├── ./11-43-22.866
│   ├── ./11-43-22.866/_current_cfFITC_02_
│   │   └── ./11-43-22.866/_current_cfFITC_02_/stack1
│   │       └── ./11-43-22.866/_current_cfFITC_02_/stack1/frame_t_0.ets
│   └── ./11-43-22.866/current_cfFITC_02.vsi
├── ./11-43-22.866.log
├── ./11-43-36.329
│   └── ./11-43-36.329/Image_01.tif
├── ./11-43-36.329.log
├── ./11-43-36.968
│   ├── ./11-43-36.968/_current_cfFITC_08_
│   │   └── ./11-43-36.968/_current_cfFITC_08_/stack1
│   │       └── ./11-43-36.968/_current_cfFITC_08_/stack1/frame_t_0.ets
│   └── ./11-43-36.968/current_cfFITC_08.vsi
├── ./11-43-36.968.log
├── ./11-43-50.656
│   └── ./11-43-50.656/Image_12.tif
├── ./11-43-50.656.log
├── ./11-43-51.219
│   ├── ./11-43-51.219/_current_cfFITC_24_
│   │   └── ./11-43-51.219/_current_cfFITC_24_/stack1
│   │       └── ./11-43-51.219/_current_cfFITC_24_/stack1/frame_t_0.ets
│   └── ./11-43-51.219/current_cfFITC_24.vsi
├── ./11-43-51.219.log
├── ./11-44-04.502
│   └── ./11-44-04.502/Image_23.tif
├── ./11-44-04.502.log
├── ./11-44-05.038
│   └── ./11-44-05.038/Image_10.tif
├── ./11-44-05.038.log
├── ./11-44-05.611
│   └── ./11-44-05.611/Image_01.tif
├── ./11-44-05.611.log
├── ./11-44-06.261
│   └── ./11-44-06.261/Image_15.tif
├── ./11-44-06.261.log
├── ./11-44-07.061
│   └── ./11-44-07.061/Image_12.tif
├── ./11-44-07.061.log
├── ./11-44-07.644
│   └── ./11-44-07.644/Image_01.tif
├── ./11-44-07.644.log
├── ./11-44-08.183
│   └── ./11-44-08.183/Image_02.tif
├── ./11-44-08.183.log
├── ./11-44-08.750
│   ├── ./11-44-08.750/_current_cfFITC_02_
│   │   └── ./11-44-08.750/_current_cfFITC_02_/stack1
│   │       └── ./11-44-08.750/_current_cfFITC_02_/stack1/frame_t_0.ets
│   └── ./11-44-08.750/current_cfFITC_02.vsi
├── ./11-44-08.750.log
├── ./11-44-23.069
│   ├── ./11-44-23.069/_current_cfFITC_13_
│   │   └── ./11-44-23.069/_current_cfFITC_13_/stack1
│   │       └── ./11-44-23.069/_current_cfFITC_13_/stack1/frame_t_0.ets
│   └── ./11-44-23.069/current_cfFITC_13.vsi
├── ./11-44-23.069.log
├── ./11-44-36.835
│   └── ./11-44-36.835/Image_13.tif
├── ./11-44-36.835.log
├── ./11-44-37.381
│   └── ./11-44-37.381/Image_14.tif
├── ./11-44-37.381.log
├── ./11-44-38.265
│   └── ./11-44-38.265/Image_09.tif
├── ./11-44-38.265.log
├── ./11-44-38.850
│   ├── ./11-44-38.850/_current_cfFITC_03_
│   │   └── ./11-44-38.850/_current_cfFITC_03_/stack1
│   │       └── ./11-44-38.850/_current_cfFITC_03_/stack1/frame_t_0.ets
│   └── ./11-44-38.850/current_cfFITC_03.vsi
├── ./11-44-38.850.log
├── ./11-44-52.970
│   ├── ./11-44-52.970/_current_cfFITC_14_
│   │   └── ./11-44-52.970/_current_cfFITC_14_/stack1
│   │       └── ./11-44-52.970/_current_cfFITC_14_/stack1/frame_t_0.ets
│   └── ./11-44-52.970/current_cfFITC_14.vsi
├── ./11-44-52.970.log
├── ./11-45-06.455
│   └── ./11-45-06.455/Image_08.tif
├── ./11-45-06.455.log
├── ./11-45-07.028
│   ├── ./11-45-07.028/_current_cfFITC_10_
│   │   └── ./11-45-07.028/_current_cfFITC_10_/stack1
│   │       └── ./11-45-07.028/_current_cfFITC_10_/stack1/frame_t_0.ets
│   └── ./11-45-07.028/current_cfFITC_10.vsi
├── ./11-45-07.028.log
├── ./11-45-20.538
│   └── ./11-45-20.538/Image_07.tif
├── ./11-45-20.538.log
├── ./11-45-21.065
│   └── ./11-45-21.065/Image_10.tif
├── ./11-45-21.065.log
├── ./11-45-21.807
│   └── ./11-45-21.807/Image_13.tif
├── ./11-45-21.807.log
├── ./11-45-22.376
│   └── ./11-45-22.376/Image_07.tif
├── ./11-45-22.376.log
├── ./11-45-22.899
│   └── ./11-45-22.899/Image_18.tif
├── ./11-45-22.899.log
├── ./11-45-23.425
│   └── ./11-45-23.425/Image_11.tif
├── ./11-45-23.425.log
├── ./11-45-23.910
│   └── ./11-45-23.910/Image_04.tif
├── ./11-45-23.910.log
├── ./11-45-24.603
│   └── ./11-45-24.603/Image_18.tif
├── ./11-45-24.603.log
├── ./11-45-25.196
│   └── ./11-45-25.196/Image_12.tif
├── ./11-45-25.196.log
├── ./11-45-25.804
│   └── ./11-45-25.804/Image_11.tif
├── ./11-45-25.804.log
├── ./11-45-26.456
│   └── ./11-45-26.456/Image_01.tif
├── ./11-45-26.456.log
├── ./11-45-27.222
│   ├── ./11-45-27.222/_current_cfFITC_08_
│   │   └── ./11-45-27.222/_current_cfFITC_08_/stack1
│   │       └── ./11-45-27.222/_current_cfFITC_08_/stack1/frame_t_0.ets
│   └── ./11-45-27.222/current_cfFITC_08.vsi
├── ./11-45-27.222.log
├── ./11-45-42.066
│   ├── ./11-45-42.066/_current_cfFITC_11_
│   │   └── ./11-45-42.066/_current_cfFITC_11_/stack1
│   │       └── ./11-45-42.066/_current_cfFITC_11_/stack1/frame_t_0.ets
│   └── ./11-45-42.066/current_cfFITC_11.vsi
├── ./11-45-42.066.log
├── ./11-45-55.840
│   ├── ./11-45-55.840/_current_cfFITC_19_
│   │   └── ./11-45-55.840/_current_cfFITC_19_/stack1
│   │       └── ./11-45-55.840/_current_cfFITC_19_/stack1/frame_t_0.ets
│   └── ./11-45-55.840/current_cfFITC_19.vsi
├── ./11-45-55.840.log
├── ./11-46-09.557
│   └── ./11-46-09.557/Image_10.tif
├── ./11-46-09.557.log
├── ./11-46-10.099
│   ├── ./11-46-10.099/_current_cfFITC_22_
│   │   └── ./11-46-10.099/_current_cfFITC_22_/stack1
│   │       └── ./11-46-10.099/_current_cfFITC_22_/stack1/frame_t_0.ets
│   └── ./11-46-10.099/current_cfFITC_22.vsi
├── ./11-46-10.099.log
├── ./11-46-23.997
│   └── ./11-46-23.997/Image_24.tif
├── ./11-46-23.997.log
├── ./11-46-24.496
│   └── ./11-46-24.496/Image_14.tif
├── ./11-46-24.496.log
├── ./11-46-25.149
│   └── ./11-46-25.149/Image_05.tif
├── ./11-46-25.149.log
├── ./11-46-25.751
│   └── ./11-46-25.751/Image_16.tif
├── ./11-46-25.751.log
├── ./12-02-58.537
│   ├── ./12-02-58.537/_1_cfTRITC, cfCY5, cfFITC_02_
│   │   └── ./12-02-58.537/_1_cfTRITC, cfCY5, cfFITC_02_/stack1
│   │       └── ./12-02-58.537/_1_cfTRITC, cfCY5, cfFITC_02_/stack1/frame_t_0.ets
│   └── ./12-02-58.537/1_cfTRITC, cfCY5, cfFITC_02.vsi
├── ./12-02-58.537.log
├── ./12-03-07.498
│   ├── ./12-03-07.498/_oisBDEB_
│   │   └── ./12-03-07.498/_oisBDEB_/stack1
│   │       └── ./12-03-07.498/_oisBDEB_/stack1/frame_t_0.ets
│   └── ./12-03-07.498/oisBDEB.vsi
├── ./12-03-07.498.log
├── ./12-03-16.096
│   ├── ./12-03-16.096/_1_cfTRITC, cfCY5, cfFITC_11_
│   │   └── ./12-03-16.096/_1_cfTRITC, cfCY5, cfFITC_11_/stack1
│   │       └── ./12-03-16.096/_1_cfTRITC, cfCY5, cfFITC_11_/stack1/frame_t_0.ets
│   └── ./12-03-16.096/1_cfTRITC, cfCY5, cfFITC_11.vsi
├── ./12-03-16.096.log
├── ./12-03-22.518
│   ├── ./12-03-22.518/_1_cfTRITC, cfCY5, cfFITC_10_
│   │   └── ./12-03-22.518/_1_cfTRITC, cfCY5, cfFITC_10_/stack1
│   │       └── ./12-03-22.518/_1_cfTRITC, cfCY5, cfFITC_10_/stack1/frame_t_0.ets
│   └── ./12-03-22.518/1_cfTRITC, cfCY5, cfFITC_10.vsi
├── ./12-03-22.518.log
├── ./12-03-28.879
│   ├── ./12-03-28.879/_1_cfTRITC, cfCY5, cfFITC_08_
│   │   └── ./12-03-28.879/_1_cfTRITC, cfCY5, cfFITC_08_/stack1
│   │       └── ./12-03-28.879/_1_cfTRITC, cfCY5, cfFITC_08_/stack1/frame_t_0.ets
│   └── ./12-03-28.879/1_cfTRITC, cfCY5, cfFITC_08.vsi
├── ./12-03-28.879.log
├── ./12-03-35.015
│   ├── ./12-03-35.015/_1_cfTRITC, cfCY5, cfFITC_05_
│   │   └── ./12-03-35.015/_1_cfTRITC, cfCY5, cfFITC_05_/stack1
│   │       └── ./12-03-35.015/_1_cfTRITC, cfCY5, cfFITC_05_/stack1/frame_t_0.ets
│   └── ./12-03-35.015/1_cfTRITC, cfCY5, cfFITC_05.vsi
├── ./12-03-35.015.log
├── ./12-03-45.033
│   ├── ./12-03-45.033/_1_cfTRITC, cfCY5, cfFITC_04_
│   │   └── ./12-03-45.033/_1_cfTRITC, cfCY5, cfFITC_04_/stack1
│   │       └── ./12-03-45.033/_1_cfTRITC, cfCY5, cfFITC_04_/stack1/frame_t_0.ets
│   └── ./12-03-45.033/1_cfTRITC, cfCY5, cfFITC_04.vsi
├── ./12-03-45.033.log
├── ./12-03-51.608
│   ├── ./12-03-51.608/_1_cfTRITC, cfCY5, cfFITC_01_
│   │   └── ./12-03-51.608/_1_cfTRITC, cfCY5, cfFITC_01_/stack1
│   │       └── ./12-03-51.608/_1_cfTRITC, cfCY5, cfFITC_01_/stack1/frame_t_0.ets
│   └── ./12-03-51.608/1_cfTRITC, cfCY5, cfFITC_01.vsi
├── ./12-03-51.608.log
├── ./12-03-59.829
│   ├── ./12-03-59.829/_ois6D2A_
│   │   └── ./12-03-59.829/_ois6D2A_/stack1
│   │       └── ./12-03-59.829/_ois6D2A_/stack1/frame_t_0.ets
│   └── ./12-03-59.829/ois6D2A.vsi
├── ./12-03-59.829.log
├── ./12-04-07.841
│   ├── ./12-04-07.841/_1_cfTRITC, cfCY5, cfFITC_07_
│   │   └── ./12-04-07.841/_1_cfTRITC, cfCY5, cfFITC_07_/stack1
│   │       └── ./12-04-07.841/_1_cfTRITC, cfCY5, cfFITC_07_/stack1/frame_t_0.ets
│   └── ./12-04-07.841/1_cfTRITC, cfCY5, cfFITC_07.vsi
├── ./12-04-07.841.log
├── ./12-04-14.744
│   ├── ./12-04-14.744/_1_cfTRITC, cfCY5, cfFITC_07_
│   │   └── ./12-04-14.744/_1_cfTRITC, cfCY5, cfFITC_07_/stack1
│   │       └── ./12-04-14.744/_1_cfTRITC, cfCY5, cfFITC_07_/stack1/frame_t_0.ets
│   └── ./12-04-14.744/1_cfTRITC, cfCY5, cfFITC_07.vsi
├── ./12-04-14.744.log
├── ./12-04-23.633
│   ├── ./12-04-23.633/_1_cfTRITC, cfCY5, cfFITC_06_
│   │   └── ./12-04-23.633/_1_cfTRITC, cfCY5, cfFITC_06_/stack1
│   │       └── ./12-04-23.633/_1_cfTRITC, cfCY5, cfFITC_06_/stack1/frame_t_0.ets
│   └── ./12-04-23.633/1_cfTRITC, cfCY5, cfFITC_06.vsi
├── ./12-04-23.633.log
├── ./12-04-30.364
│   ├── ./12-04-30.364/_1_cfTRITC, cfCY5, cfFITC_06_
│   │   └── ./12-04-30.364/_1_cfTRITC, cfCY5, cfFITC_06_/stack1
│   │       └── ./12-04-30.364/_1_cfTRITC, cfCY5, cfFITC_06_/stack1/frame_t_0.ets
│   └── ./12-04-30.364/1_cfTRITC, cfCY5, cfFITC_06.vsi
├── ./12-04-30.364.log
├── ./12-04-37.059
│   ├── ./12-04-37.059/_1_cfTRITC, cfCY5, cfFITC_10_
│   │   └── ./12-04-37.059/_1_cfTRITC, cfCY5, cfFITC_10_/stack1
│   │       └── ./12-04-37.059/_1_cfTRITC, cfCY5, cfFITC_10_/stack1/frame_t_0.ets
│   └── ./12-04-37.059/1_cfTRITC, cfCY5, cfFITC_10.vsi
├── ./12-04-37.059.log
├── ./12-04-43.806
│   ├── ./12-04-43.806/_1_cfTRITC, cfCY5, cfFITC_09_
│   │   └── ./12-04-43.806/_1_cfTRITC, cfCY5, cfFITC_09_/stack1
│   │       └── ./12-04-43.806/_1_cfTRITC, cfCY5, cfFITC_09_/stack1/frame_t_0.ets
│   └── ./12-04-43.806/1_cfTRITC, cfCY5, cfFITC_09.vsi
├── ./12-04-43.806.log
├── ./12-04-51.658
│   ├── ./12-04-51.658/_1_cfTRITC, cfCY5, cfFITC_08_
│   │   └── ./12-04-51.658/_1_cfTRITC, cfCY5, cfFITC_08_/stack1
│   │       └── ./12-04-51.658/_1_cfTRITC, cfCY5, cfFITC_08_/stack1/frame_t_0.ets
│   └── ./12-04-51.658/1_cfTRITC, cfCY5, cfFITC_08.vsi
├── ./12-04-51.658.log
├── ./12-04-57.811
│   ├── ./12-04-57.811/_1_cfTRITC, cfCY5, cfFITC_01_
│   │   └── ./12-04-57.811/_1_cfTRITC, cfCY5, cfFITC_01_/stack1
│   │       └── ./12-04-57.811/_1_cfTRITC, cfCY5, cfFITC_01_/stack1/frame_t_0.ets
│   └── ./12-04-57.811/1_cfTRITC, cfCY5, cfFITC_01.vsi
├── ./12-04-57.811.log
├── ./12-05-04.429
│   ├── ./12-05-04.429/_1_cfTRITC, cfCY5, cfFITC_09_
│   │   └── ./12-05-04.429/_1_cfTRITC, cfCY5, cfFITC_09_/stack1
│   │       └── ./12-05-04.429/_1_cfTRITC, cfCY5, cfFITC_09_/stack1/frame_t_0.ets
│   └── ./12-05-04.429/1_cfTRITC, cfCY5, cfFITC_09.vsi
├── ./12-05-04.429.log
├── ./12-05-12.073
│   ├── ./12-05-12.073/_1_cfTRITC, cfCY5, cfFITC_02_
│   │   └── ./12-05-12.073/_1_cfTRITC, cfCY5, cfFITC_02_/stack1
│   │       └── ./12-05-12.073/_1_cfTRITC, cfCY5, cfFITC_02_/stack1/frame_t_0.ets
│   └── ./12-05-12.073/1_cfTRITC, cfCY5, cfFITC_02.vsi
├── ./12-05-12.073.log
├── ./12-05-20.118
│   ├── ./12-05-20.118/_1_cfTRITC, cfCY5, cfFITC_05_
│   │   └── ./12-05-20.118/_1_cfTRITC, cfCY5, cfFITC_05_/stack1
│   │       └── ./12-05-20.118/_1_cfTRITC, cfCY5, cfFITC_05_/stack1/frame_t_0.ets
│   └── ./12-05-20.118/1_cfTRITC, cfCY5, cfFITC_05.vsi
├── ./12-05-20.118.log
├── ./12-05-27.539
│   ├── ./12-05-27.539/_1_cfTRITC, cfCY5, cfFITC_03_
│   │   └── ./12-05-27.539/_1_cfTRITC, cfCY5, cfFITC_03_/stack1
│   │       └── ./12-05-27.539/_1_cfTRITC, cfCY5, cfFITC_03_/stack1/frame_t_0.ets
│   └── ./12-05-27.539/1_cfTRITC, cfCY5, cfFITC_03.vsi
├── ./12-05-27.539.log
├── ./12-05-34.074
│   ├── ./12-05-34.074/_1_cfTRITC, cfCY5, cfFITC_04_
│   │   └── ./12-05-34.074/_1_cfTRITC, cfCY5, cfFITC_04_/stack1
│   │       └── ./12-05-34.074/_1_cfTRITC, cfCY5, cfFITC_04_/stack1/frame_t_0.ets
│   └── ./12-05-34.074/1_cfTRITC, cfCY5, cfFITC_04.vsi
├── ./12-05-34.074.log
├── ./12-05-41.223
│   ├── ./12-05-41.223/_ois4476_
│   │   └── ./12-05-41.223/_ois4476_/stack1
│   │       └── ./12-05-41.223/_ois4476_/stack1/frame_t_0.ets
│   └── ./12-05-41.223/ois4476.vsi
├── ./12-05-41.223.log
├── ./12-05-50.159
│   ├── ./12-05-50.159/_1_cfTRITC, cfCY5, cfFITC_10_
│   │   └── ./12-05-50.159/_1_cfTRITC, cfCY5, cfFITC_10_/stack1
│   │       └── ./12-05-50.159/_1_cfTRITC, cfCY5, cfFITC_10_/stack1/frame_t_0.ets
│   └── ./12-05-50.159/1_cfTRITC, cfCY5, cfFITC_10.vsi
├── ./12-05-50.159.log
├── ./12-05-56.740
│   ├── ./12-05-56.740/_1_cfTRITC, cfCY5, cfFITC_12_
│   │   └── ./12-05-56.740/_1_cfTRITC, cfCY5, cfFITC_12_/stack1
│   │       └── ./12-05-56.740/_1_cfTRITC, cfCY5, cfFITC_12_/stack1/frame_t_0.ets
│   └── ./12-05-56.740/1_cfTRITC, cfCY5, cfFITC_12.vsi
├── ./12-05-56.740.log
├── ./12-06-03.867
│   ├── ./12-06-03.867/_1_cfTRITC, cfCY5, cfFITC_11_
│   │   └── ./12-06-03.867/_1_cfTRITC, cfCY5, cfFITC_11_/stack1
│   │       └── ./12-06-03.867/_1_cfTRITC, cfCY5, cfFITC_11_/stack1/frame_t_0.ets
│   └── ./12-06-03.867/1_cfTRITC, cfCY5, cfFITC_11.vsi
├── ./12-06-03.867.log
├── ./12-06-10.390
│   ├── ./12-06-10.390/_1_cfTRITC, cfCY5, cfFITC_05_
│   │   └── ./12-06-10.390/_1_cfTRITC, cfCY5, cfFITC_05_/stack1
│   │       └── ./12-06-10.390/_1_cfTRITC, cfCY5, cfFITC_05_/stack1/frame_t_0.ets
│   └── ./12-06-10.390/1_cfTRITC, cfCY5, cfFITC_05.vsi
├── ./12-06-10.390.log
├── ./12-06-16.631
│   ├── ./12-06-16.631/_1_cfTRITC, cfCY5, cfFITC_02_
│   │   └── ./12-06-16.631/_1_cfTRITC, cfCY5, cfFITC_02_/stack1
│   │       └── ./12-06-16.631/_1_cfTRITC, cfCY5, cfFITC_02_/stack1/frame_t_0.ets
│   └── ./12-06-16.631/1_cfTRITC, cfCY5, cfFITC_02.vsi
├── ./12-06-16.631.log
├── ./12-06-24.405
│   ├── ./12-06-24.405/_1_cfTRITC, cfCY5, cfFITC_06_
│   │   └── ./12-06-24.405/_1_cfTRITC, cfCY5, cfFITC_06_/stack1
│   │       └── ./12-06-24.405/_1_cfTRITC, cfCY5, cfFITC_06_/stack1/frame_t_0.ets
│   └── ./12-06-24.405/1_cfTRITC, cfCY5, cfFITC_06.vsi
├── ./12-06-24.405.log
├── ./12-06-30.971
│   ├── ./12-06-30.971/_ois47EA_
│   │   └── ./12-06-30.971/_ois47EA_/stack1
│   │       └── ./12-06-30.971/_ois47EA_/stack1/frame_t_0.ets
│   └── ./12-06-30.971/ois47EA.vsi
├── ./12-06-30.971.log
├── ./12-06-41.116
│   ├── ./12-06-41.116/_1_cfTRITC, cfCY5, cfFITC_08_
│   │   └── ./12-06-41.116/_1_cfTRITC, cfCY5, cfFITC_08_/stack1
│   │       └── ./12-06-41.116/_1_cfTRITC, cfCY5, cfFITC_08_/stack1/frame_t_0.ets
│   └── ./12-06-41.116/1_cfTRITC, cfCY5, cfFITC_08.vsi
├── ./12-06-41.116.log
├── ./12-06-47.564
│   ├── ./12-06-47.564/_1_cfTRITC, cfCY5, cfFITC_07_
│   │   └── ./12-06-47.564/_1_cfTRITC, cfCY5, cfFITC_07_/stack1
│   │       └── ./12-06-47.564/_1_cfTRITC, cfCY5, cfFITC_07_/stack1/frame_t_0.ets
│   └── ./12-06-47.564/1_cfTRITC, cfCY5, cfFITC_07.vsi
├── ./12-06-47.564.log
├── ./12-06-53.931
│   ├── ./12-06-53.931/_1_cfTRITC, cfCY5, cfFITC_07_
│   │   └── ./12-06-53.931/_1_cfTRITC, cfCY5, cfFITC_07_/stack1
│   │       └── ./12-06-53.931/_1_cfTRITC, cfCY5, cfFITC_07_/stack1/frame_t_0.ets
│   └── ./12-06-53.931/1_cfTRITC, cfCY5, cfFITC_07.vsi
├── ./12-06-53.931.log
├── ./12-07-00.715
│   ├── ./12-07-00.715/_1_cfTRITC, cfCY5, cfFITC_02_
│   │   └── ./12-07-00.715/_1_cfTRITC, cfCY5, cfFITC_02_/stack1
│   │       └── ./12-07-00.715/_1_cfTRITC, cfCY5, cfFITC_02_/stack1/frame_t_0.ets
│   └── ./12-07-00.715/1_cfTRITC, cfCY5, cfFITC_02.vsi
├── ./12-07-00.715.log
├── ./12-07-07.283
│   ├── ./12-07-07.283/_oisF05F_
│   │   └── ./12-07-07.283/_oisF05F_/stack1
│   │       └── ./12-07-07.283/_oisF05F_/stack1/frame_t_0.ets
│   └── ./12-07-07.283/oisF05F.vsi
├── ./12-07-07.283.log
├── ./12-07-17.443
│   ├── ./12-07-17.443/_1_cfTRITC, cfCY5, cfFITC_11_
│   │   └── ./12-07-17.443/_1_cfTRITC, cfCY5, cfFITC_11_/stack1
│   │       └── ./12-07-17.443/_1_cfTRITC, cfCY5, cfFITC_11_/stack1/frame_t_0.ets
│   └── ./12-07-17.443/1_cfTRITC, cfCY5, cfFITC_11.vsi
├── ./12-07-17.443.log
├── ./12-07-23.951
│   ├── ./12-07-23.951/_1_cfTRITC, cfCY5, cfFITC_05_
│   │   └── ./12-07-23.951/_1_cfTRITC, cfCY5, cfFITC_05_/stack1
│   │       └── ./12-07-23.951/_1_cfTRITC, cfCY5, cfFITC_05_/stack1/frame_t_0.ets
│   └── ./12-07-23.951/1_cfTRITC, cfCY5, cfFITC_05.vsi
├── ./12-07-23.951.log
├── ./12-07-30.487
│   ├── ./12-07-30.487/_1_cfTRITC, cfCY5, cfFITC_04_
│   │   └── ./12-07-30.487/_1_cfTRITC, cfCY5, cfFITC_04_/stack1
│   │       └── ./12-07-30.487/_1_cfTRITC, cfCY5, cfFITC_04_/stack1/frame_t_0.ets
│   └── ./12-07-30.487/1_cfTRITC, cfCY5, cfFITC_04.vsi
├── ./12-07-30.487.log
├── ./12-07-36.811
│   ├── ./12-07-36.811/_1_cfTRITC, cfCY5, cfFITC_01_
│   │   └── ./12-07-36.811/_1_cfTRITC, cfCY5, cfFITC_01_/stack1
│   │       └── ./12-07-36.811/_1_cfTRITC, cfCY5, cfFITC_01_/stack1/frame_t_0.ets
│   └── ./12-07-36.811/1_cfTRITC, cfCY5, cfFITC_01.vsi
├── ./12-07-36.811.log
├── ./12-07-42.842
│   ├── ./12-07-42.842/_2_cfTRITC, cfCY5, cfFITC_10_
│   │   └── ./12-07-42.842/_2_cfTRITC, cfCY5, cfFITC_10_/stack1
│   │       └── ./12-07-42.842/_2_cfTRITC, cfCY5, cfFITC_10_/stack1/frame_t_0.ets
│   └── ./12-07-42.842/2_cfTRITC, cfCY5, cfFITC_10.vsi
├── ./12-07-42.842.log
├─

But moreover what we noticed is that some files are missing, like the OEX file where some metadata acquisition info is stored.

This is a big problem for us, even because the extra question is: which files are not imported? only the .oex?

Are we doing something wrong?
How do you save raw data (including not images data) in an Imaging Facility where you could have many different scenarios in terms of acquisition types, of user preferences of saving files, of microscopes and formats?
Is it not the purpose of Omero to be a data storage but it’s more useful as a viewer?

Sorry to stress you,
and thanks a lot for the promptness and follow up
Emanuele

[joshmoore]

Hi Emanuele,

@emartini

But moreover what we noticed is that some files are missing, like the OEX file where some metadata acquisition info is stored.

Going back to my comment above, OEX is not a format supported by Bio-Formats. You can see the current list here: https://docs.openmicroscopy.org/bio-formats/6.5.1/supported-formats.html

@emartini

Are we doing something wrong?

No. But there is not immediately support for every format. Please see http://blog.openmicroscopy.org/community/file-formats/2019/06/25/formats/ etc.

@emartini

How do you save raw data (including not images data) in an Imaging Facility where you could have many different scenarios in terms of acquisition types, of user preferences of saving files, of microscopes and formats?

This would depend on what all you are trying to store. Certainly, for example, it would be useful to overlay the ROIs on top of the images rather than having them as separate TIFFs. That’s certainly something a supported format could do. Alternatively, it could be done after the fact via script.

In your case, though, if you want to move forward with OMERO, the first step would be to have the image data structured as you want, since I’m not sure from your screenshots if the time lapses are even being properly grouped together. Then you could layer further data on top of that.

@emartini

Is it not the purpose of Omero to be a data storage but it’s more useful as a viewer?

It definitely is. But again, Bio-Formats and by extension OMERO can’t a priori know everything about every file format. Support would either need to be added for that format or your data would need to be converted into a supported format. It might be that the microscopy provides an option for exporting to OME-TIFF which you could try. Otherwise, there are a number of examples at the moment for converting from proprietary to OME-TIFF (see Converting Whole Slide Images to OME-TIFF: A New Workflow) which might also work.

@emartini

Sorry to stress you,
and thanks a lot for the promptness and follow up

Don’t worry. You’re not the cause of stress. In general, our community has a clear file format issue that we all need to find a solution for together.

~Josh

[lguerard]

Hi all,

@emartini I’m also now having an issue while trying to download the raw data from OMERO with VSI files.

If I understood correctly from the acquisition side, there is only one VSI file and a second file which contains all the tiles of the acquisition. When uploading to OMERO however, all these tiles are split and I can’t manage to get back the single input file. Did you face this issue as well and did you find a way to handle this case ?

Thanks !

[emartini (Emanuele Martini)]

dear @lguerard ,
we faced this (together with other similar issues, with other kinds of files) and we decided to not proceed to implement Omero for our Institute Imaging Unit.
It was a test, and we then decided to use a more “normal” server dedicated to the Imaging Users and maybe use Omero for specific tasks but not for Imaging Unit sharing images general purpose.

[lguerard]

I understand, I’ll wait to see if maybe someone from the OME has any ideas about how to deal with this.

Thanks for your help