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WU-BIMAC / NBOMicroscopyMetadataSpecs

The 4DN + BINA Tiered System of Microscopy Metadata Guidelines was developed by the 4DN Imaging Standards Working Group in collaboration with the BINA Data Management and Quality Control Working Group (https://www.bioimagingna.org/qc-dm-wg) for documenting microscopy experiments and assessing the quality of image data.
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Giang -- Add to spinning disk: disk pinhole size and spacing, bypass?, excitation homogenizer? #70

Open WillGiang opened 2 years ago

WillGiang commented 2 years ago

Extension name (optional): 4DN-BINA OME Advanced + Confocal extension

Element name(s): NBOA:SpinningDisk

Field name(s):

Justification for the addition (brief and compelling):

DiskPinholeDiamater and DiskPinholeSpacing The optical sectioning provided by a spinning disk confocal is a function of the disk design and cannot be adjusted like a laser scanning microscope. The Yokogawa CSU-X1 is designed for high NA objectives and does a great job with thin samples. However, when imaging thicker samples, pinhole crosstalk becomes an issue. Increasing the spacing between pinholes will decrease light throughput but allow for better image quality with thicker samples. People seeking to purchase newer spinning disk units can have the option of different disks.

DiskBypass In some spinning disk models, the disk cannot be moved out of the light path for widefield/brightfield imaging. The presence of the disk also slightly impacts DIC quality.

HomogenizedExcitation Some spinning disk scopes suffer from inhomogeneous excitation. There are:

Full description of the proposed addition (enough detail to implement): DiskPinholeDiameter: This records (in microns) the diameter of the spinning disk's pinholes. DiskPinholeSpacing: This records (in microns) the spacing between the spinning disk pinholes. DiskBypass: This records whether the spinning disk has the ability (manual or motorized) to remove the disk from the light path. HomogenizedExcitation: This records whether the excitation for the spinning disk is homogenous (whether innately or through an add-on).

- New Element/Field name(s): __ DiskPinholeDiameter DiskPinholeSpacing DiskBypass HomogenizedExcitation

strambc commented 2 years ago

Hi @WillGiang thank you for your input on this very important topic. I wanted to let you know that the current process for revising the model is to go through a series of community conversations involving manufacturers, experts in the field, and members of the relevant QUAREP-LiMI WG.

We are currently involved in this process with respect to Camera (which is a specialization of Detector). The next items we are planning to address are:

It will be great if you could participate to the relevant conversations related to this issue. I will make sure to keep you posted on when they are going to happen.

strambc commented 2 years ago

@WillGiang

The ISSUE has been recorded in the work in progress document.

One clarification?

Do you think "HomogenizedExcitation" should be a Hardware Specification or Acquisition Settings?

In other words, can the homogenization be applied yes or no during acquisition, or once it is in place it is always present during all acquisitions?

WillGiang commented 2 years ago

Hi @strambc ,

I imagined HomogenizedExcitation as a Hardware Specification since once it's in place, it's always present during all acquisitions.

While acquisition software can offer a computational shading correction, it's not functionally equivalent to having more uniform excitation. An extreme example would be in single molecule localization microscopy where the blinking rate differs based on laser power.

Thanks for keeping the momentum going on this!