Data Management

Your place to discuss general handling of images and the CZI file format
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user-6164
Posts: 1
Joined: Thu Jan 01, 1970 1:00 am

Data Management

Post by user-6164 »

Hello,

We recently acquired an XRM 520 Versa at the University of Colorado Boulder. I am one of the PhD students that will help run the instrument as in a core facility setting, having industry and academic collaborators scan their sample. Does anyone have recommendations of how to handle data? Do you keep only txrm files? for how long? where to keep them? is there a way/ program to automate this process?

Any insight would be really helpful. Thank you so much :)
user-8
Posts: 63
Joined: Thu Jan 01, 1970 1:00 am

Post by user-8 »

Hi,

I am not sure if I can actually give a meaningful answer here, since this is the ZEN Blue OAD forum. Nevertheless here some comments.

  • Versa is not running in ZEN Blue etc. and therefore has no OAD --> this is why this may be the wrong forum
  • ZEN Blue can import TXM files by converting them into official CZIs, the official ZEISS data format.
  • By doing so you can make use of all the nice features of the ZEN Blue / ZEN Core software
  • Especially interesting might be
    • the 3DxL viewer
    • ZEN Intellesis Trainable Segmentation
All those things are possible in ZEN after TXM Import.

To come back to your original questions ...

  • How long --> is up to you, but at least 5 years
  • Where --> Server or database (OMERO?)
  • Which Format? --> I would keep the raw TXM and convert to CZI or OME-TIFF for processing
Martin Stas
Posts: 11
Joined: Mon Jun 19, 2023 12:04 pm

Re: Data Management

Post by Martin Stas »

Hey there, fellow science enthusiasts! It's fantastic to see your dedication to managing data effectively with the XRM 520 Versa. I totally get how crucial it is to handle data efficiently, especially in a bustling core facility.

Speaking from my experience, maintaining a structured approach can make your life a breeze. Consider storing not just the txrm files, but also any associated metadata in a well-organized manner. Utilizing a hierarchical folder structure or a dedicated database can help keep everything neat and easily retrievable.

Now, about automation, oh boy, it's a game-changer! Tools like scripting languages (Python, anyone?) can help automate data processing and organization. Plus, setting up regular backups, perhaps on a secure server or cloud platform, can be a lifesaver in case of unforeseen glitches.

As for user-6164, a golden nugget of advice would be to collaborate closely with your IT department. They might have insights into the best practices and tools specifically tailored to your university's environment.
Devyn Waters
Posts: 1
Joined: Thu Aug 17, 2023 8:18 am

Re: Data Management

Post by Devyn Waters »

Benelli M2 is expected to lose value in the upcoming years; invest in a location with greater promise than mr mine. It is encouraging.
Branden= Curtis
Posts: 1
Joined: Fri Aug 25, 2023 6:56 am

Re: Data Management

Post by Branden= Curtis »

Databases are optimized to deal with massive volumes of data. If you keep it in text files, you'll have to write your own code to perform the same thing, and it will be less efficient, I promise. The information contained in the text files should be saved as a VARCHAR(8000) or Blob inside the relevant database table.

Benefits of storing information in a database includethe backrooms:

- You only need one spot to keep all of your information. You can easily make copies and restore them elsewhere if necessary.
- Databases inherently support concurrency, thus even if multiple users simultaneously access the same data in the same table or row, the database will manage the situation.
- A distributed storage strategy that combines file and database management necessitates rigorous consistency checks.
- Use UPDATE if you just care about archiving the most recent changes to a text file. SCD Type 2 storage or a historical table containing older text file data is the way to go if you want to maintain track of what was contained in those files throughout time.
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