Update on microscopy data management.

Following on from my earlier post….

While I decide whether we need anything further I have developed a Word form for the lab to use for each imaging experiment. It has a built in date stamp,drop boxes for commonly used antibodies and cell labels and customized content for our most commonly used imaging systems. I had no idea how to make forms in Word but it seems pretty easy; this also means it will be easy to adapt over time. We might reject this idea or use it for the next 10 years – time will tell.

I’ve attached this finalized draft: Experiment Log 2012a in case it is of any use to anyone else. It is read only such that the user gets to change the filename. The date in the top right should auto update as well. the idea is that the “user” saves this along with the image. Frighteningly simple but hopefully so simple it will be effective. Also something that I hope will be usable from undergrad to Professor.

Should you wish to adapt this for your self you will probably need to use this editable version: Experiment Log 2012 template unprotected.


2 thoughts on “Update on microscopy data management.

  1. This seems like a good start, and will hopefully allow an accurate record and log of those experiments to be kept. I think this is just one step away from using a template html page, using a very similar format, but which then links to the images taken. Lots of things stay the same as they are now (dated folder architecture) with the advantage that links can be made directly to the images. Everything is stored on a server (accessible either locally or through www if you wish), can be backed up simply and should be (relatively) futureproof. We have a similar system in place for all our microscopy development, and to show something in a labmeeting, its all done through the server (Student: i think it showed this, PI: really, why?? Student: click the link and have a look.). We use seamonkey as a WYSIWYG html editor.

    • So what’s the HTML database…written yourselves? This is the bit I don’t know how to do despite the useful help and pointers from elsewhere. What do you have – a web entry form that is then saved to the server? Do you create the link to the image folder yourselves? I just don’t know enough about HTML folder/file structure etc to start in on this. Guessing XML is the way forward but then I am even more lost.

      Actually, when I think about this- its OMERO isn’t it…wonder if I can find a day to play…

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