Re: [micro-manager-general] Reslicing a dataset to a given time range

[Chris W. <cwe...@ms...>]

Hi Thomas,

On Fri, Jan 22, 2016 at 10:44 AM, julou <tho...@no...> wrote:

> Hi Chris,
>
> Sorry for the delayed answer…
>
> I would really appreciate to achieve the same task with datasets stored on
>> disk.
>>
> Could you please clarify what you mean by setting the name of the
> acquisition? This could refer to a number of different things in µManager
> 1.4, some of which are obsolete in µManager 2.0. At a guess, if you're
> talking about the image window's title, you can set a custom title for any
> DisplayWindow by calling DisplayWindow.setCustomTitle(). So for example,
> for the above script you could add this line:
>
> newDisplay.setCustomTitle(“Sliced timepoints from " + minTime + " through
> " + maxTime);
>
>
> Yes, I meant the name of the dataset that is used e.g. to save it on disk…
>

Ahh. That is derived from the "prefix" property of the SummaryMetadata. In
order for the Multipage TIFF to use it, you need to set the summary
metadata prior to any calls to newData.putImage(). For example:

// Copy summary metadata across. Adjust filename prefix as needed.
oldSummary = oldData.getSummaryMetadata();
newSummary = oldSummary.copy().prefix("MyPrefix").build();
newData.setSummaryMetadata(newSummary);

You should then not call setSummaryMetadata later in the script. I've
attached an updated script that incorporates this change.


>
> As for the file size, what kind of images are you putting into the
> datastore? 2k x 2k? 512x512? It'd also be worth making certain that you're
> using the most recent version of µManager 2.0; the "beta-2" build is now
> fairly out of date.
>
>
> up to 2k x 2k. Typically 1200x2048
> I was using a recent nightly built (updated since then…)
>

Very strange. What is the dimensionality of the original dataset, and of
the resliced dataset? I'm not able to reproduce this locally.


>
> Again, a script example that would do the same with datasets stored on
> disk would be really helpful!
> Thank you in advance for your help,
>

No problem. Please see the attached script.

-Chris