Questions about tutorial: FISH in C. elegans

[labnanocell]

Hi,

I’m following the tutorial/pipeline and got stuck on the calibration instruction in the NamesAndTypes step.

The text says:
“The relative pixel spacing was provided and is 0.162 µm in x and y and 0.200 µm in z. To run the calibration file please change the relative pixel spacing to 1×1×1 µm.”

In the screenshot, the settings are shown as 0.162 µm (x and y) and 0.200 µm (z), so I’m not sure what I’m supposed to do with the "To run the calibration file please change the relative pixel spacing to 1×1×1 µm."

Could you clarify what run the calibration means in the tutorial, and what should I do with this information?

Thanks!
Bispo

[labnanocell]

One little thing, I noticed a mismatch between the tutorial and the provided .cppipe pipeline for the ExportToSpreadsheet module.

The tutorial instructs:
• “Add image file and folder names to your object data file:” No

But in the provided pipeline, this setting is set to Yes.

Which one is the intended/correct setting for this exercise, and should we update either the tutorial text or the pipeline to match?

Thanks!

[bethac07]

The backstory here is that the group that designed the study that this tutorial is based on asked for pipelines or workflows that could be run both on some synthetic images, and a calibration image - you can see it in the files distributed in the screenshot below. While we originally designed this workflow for that "challenge", we probably don't need for most users to ship or mention the calibration image, it just hasnt' been on anyone's radar to do the work to edit it. If you're up for it, feel free!

I would update the pipeline re: file and folder names, fine to have it set to no. Thanks!

[labnanocell]

I removed references to the calibration file from the tutorial translation and submitted a PR with the updated pipeline.