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. Author manuscript; available in PMC: 2022 Nov 14.
Published in final edited form as: Nat Protoc. 2022 Jan 12;17(2):476–512. doi: 10.1038/s41596-021-00653-8

Table 1 |.

Recommended microscope components

Component Recommended Options Description
Microscope body Nikon Ti2 Large field-of-view and fast stage reduce acquisition time; note that custom sizing of filters may be required
Control software Micro-Manager Micro-Manager is open source and freely available; however, NIS Elements allows more flexibility, such as easier definition of imaging sites, improved alignment and autofocusing options, and saving of imaging workflows using the JOBS module
NIS Elements with JOBS module
Camera Iris 9 (Teledyne Photometrics);
Sensor: 12.58 × 12.58 mm;
2960 × 2960 pixels
The goal is to have a sensor area large enough to take advantage of the full field-of-view of the microscope. For cameras with smaller sensor areas, a 0.7X relay lens coupler can be used (e.g., Nikon, cat. no. MQD42075), although this decreases resolution and may result in vignetting.
ORCA-Flash4.0 v3 (Hamamatsu Photonics);
Sensor: 13.31 × 13.31 mm;
2048 × 2048 pixels
ORCA-Fusion (Hamamatsu Photonics);
Sensor: 14.98 × 14.98 mm;
2304 × 2304 pixels
Objective Lenses 10X air NA 0.45 (e.g., Nikon, cat. no. MRD00105) For SBS and some phenotype image acquisition
20X air NA 0.75 (e.g., Nikon, cat. No. MRD00205) Optional for phenotype image acquisition