Methods generator

Choose the microscope and hardware you used to build a draft microscopy methods paragraph, then add your acquisition settings and review the text before publication. The draft follows the QUAREP-LiMi minimal reporting recommendations for light microscopy (Better reporting is better science).

Generate the draft when you acquire the images

The generator reflects the facility record available now; it does not reconstruct earlier microscope configurations. We therefore recommend generating and saving the Methods draft at the time of image acquisition, together with the raw image metadata. Historical configuration support can be added later when the repository has an explicit time-versioned configuration model.

Microscope -- Choose an instrument --

Details to confirm

Some instrument details needed for this draft are not yet recorded. Check the items below with AIC Turku staff before publication.

Acquisition or figure reference (optional)

Review available Virtual Microscope plan

I reviewed this plan and confirm that these were the settings actually used. Include them in the draft.

Confirmed acquisition actions

Select only statements that describe what you actually did. Installed capabilities are not included automatically.

Imaging method

Tick everything you actually did for this acquisition — several methods can describe one image set, for example brightfield alongside fluorescence. Your choice decides which light paths and optical components are offered below; it does not restrict you to one of them.

Which physical path was used

One of the methods above is recorded on more than one physical path, and the hardware differs between them. Choose the one this acquisition actually used.

Readouts

Additional measurements this light path can record, beyond the imaging method itself — tick any that this acquisition also captured.

Hardware modules and environmental control

Scanner

Objectives

Light sources

Filters and dichroics

Tick each filter, dichroic or cube the acquisition used — several per wheel or turret where the experiment used several channels. The recorded transmission bands are written into the draft alongside the catalogue number.

Camera and emission splitters

Detectors

Magnification changers

Optical modulators

Illumination control

Add to methods Start another acquisition

Changing a selection after adding corrects that acquisition. Use Start another acquisition — or give a new acquisition reference — when the next entry describes a different image set.

Recover acquisition settings from image metadata

Exact exposure times, pixel size, z-step, laser settings, and other acquisition parameters are often stored in the original image metadata. In Fiji/ImageJ, open the raw file and use Image > Show Info... (or press I) to inspect the metadata. Copy the relevant values into your records. If you use an assistant to extract fields from metadata text, verify every value against the raw metadata before publication.

Generated methods draft

Add to methods commits the acquisition you have described. Correcting a selection and adding again updates that same entry rather than duplicating it; Start another acquisition clears every selection and starts a separate entry. A new acquisition reference, or changing the imaging method, also starts a separate entry and clears the hardware selections, keeping only the imaging method so you can correct it. Clear all empties the draft and every selection, including the confirmed actions and any reviewed Virtual Microscope plan. Save the draft with the acquisition records while the selected configuration is current. Finished Methods prose is kept separate from a Review before publication block listing every acquisition detail that still needs to be specified or verified; requests that apply to the whole section are stated once at the end rather than repeated under every acquisition.

Select an instrument, then choose “Add to methods”.

Copy draft Clear all Copied