NIS elements acquisition software

First draft of simple guide to get started

dOPM_Shared_NIS_binaries

Use the pdfs hyperlinked below as guides while running NIS-elements and having imported the binaries.

This readme needs directions on how to organise a JOBS database.

worth noting that this is all Nikon NIS-Elements functionality so can be looked up in NIS-Elements help documentation.

Introduction

The screenshot below shows JOBS explorer within NIS-Elements. Familiarise youreself with this and the use of JOBS scripts by using the help documentation within NIS-Elements.

The scripts in the screenshots are some simple routines we routinely use.

A typical acquisition would consist of the following in this order:

With x4/10x/20x, long working distance, air objectives: 1 - get plate z profile: uses GetPlateZProfile.bin 2 - do prefind with brightfield wide-field imaging 3 - manually select regions of interest from prefind data

Switch to water immersion 60X objective 4 - adjust prefind position list of regions of interest so all regions are centred in xyz on microscopes frames dOPM acquisition volume space: uses PrefindPoints.bin 5 - image beads before acquisition: uses dOPM_acquisition.bin 6 - do brightfield 60x images of region of interest point list: uses Brightfield.bin 7 - do dOPM timelapse acquisition of region of interest point list: uses dOPM_acquisition.bin 8 - do brightfield 60x images of region of interest point list: uses Brightfield.bin 9 - image beads after acquisition: uses dOPM_acquisition.bin

Notes to worry about for another day: Ideally the multiwell plate will have a well with beads in 3D Ideally some sample will not be timelapse imaged so you can control for light-dose

How to import and export .bin files

Import

Use the yellow icon with the arrow to import .bin files from this repo into NIS-Elements

Export

Right click on the JOBS scripts explorer window space to export .bin files from NIS0-Elements

Guides to using the scripts in this repo:

• Get Plate Z Profile : uses GetPlateZProfile.bin

• Generate point list from prefind acquisition - tile scan, zstacks of wells of interest : uses PrefindPoints.bin

• Collect brightfield images of regions of interest from point list : uses Brightfield.bin

• Acquire beads for dOPM view registration - beads : uses dOPM_acquisition.bin

• Acquire data, multipoint, dOPM, multicolor timelapse acquisition - data : uses dOPM_acquisition.bin

• Adjust focus on points - refine point list for dOPM : uses AdjustFocusOnPoints.bin

Detailed notes - work in progress

Introduction

The hardware control is based around Nikons NIS-Elements software. https://www.microscope.healthcare.nikon.com/products/software/nis-elements

I've uploaded the pdf manual for the version we use. Also the software comes with a help tool that you should become familiar with when learning how to use the system as all definitions are provided through this.

Mach3Manual: Software reference

• Getting Started
• NIS elements: hardware configuration
• NIS elements: optical configuration
• NIS elements: macros
• NIS elements: Ti2 configuration
• NIS elements: initiating stage
• NIS elements: system diagnostics
• NIS elements: position-lists
• NIS elements: ND-acquisition
• NIS elements: JOBs
• NIS elements: Perfect Focus-(PFS)
• NIS elements: Wide-field-imaging
• NIS elements: dOPM-imaging
• NIS elements: XYZ control
• NIS elements: Experiment-checklist
• NIS elements: Multi-point acquisitions
• NIS elements: Time-lapse acquisitions
• Light-sheets-mirror-control
• Laser-controls
• dOPM scanning mirrors control
• deskewing and fusing data

For developers