4Deep HoloSea S7 User manual

HoloSea Microscope User Guide
Model S7

Notices
Copyright © 4Deep inwater imaging 2018
No part of this document may be reproduced
in any format without prior agreement or writ-
ten consent from 4 Deep inwater imaging.
This software/hardware is proprietary to
4Deep inwater imaging and the company
hereby grants the customer a nonexclusive li-
cense for its use. The Customer will not mod-
ify, adapt, translate, create derivative works,
disassemble, decompile or reverse engineer
the software/hardware provided. No title to
or ownership of the software/hardware or in-
tellectual property rights are transferred to the
customer.
This software/hardware is provided “as is”,
and is subject to change, without further no-
tice in future editions.
Edition
HoloSea Microscope User Guide - Model S7
4Deep inwater imaging
6589 Chebucto Road
Halifax Nova Scotia
Canada B3L 1L9
Safety and Information Notices
An “Important” signifies helpful information in
using the software/hardware. It identifies an
important piece of information to guide the
user in their workflow, and if not followed could
result in time wasted.
A “Caution” signifies a hazard. It identifies an
operating procedure, or step, that if not fol-
lowed precisely, could result in damage to the
product or loss of information. Do not continue
beyond a “Caution” sign until the procedure is
fully understood.
A “Warning” signifies a hazard. It identifies
an operating procedure, or step, that if not fol-
lowed precisely, could result in personal injury.
Do not continue beyond a “Warning” sign until
the procedure is fully understood.
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HoloSea Microscope
iii

CONTENTS
Contents
1 Overview 1
1.1 Purpose .......................................... 1
1.2 Benefits........................................... 1
2 Introduction 2
2.1 SafetyInformation ..................................... 2
2.2 Compatibility ........................................ 2
2.3 ComponentsoftheSystem ................................ 3
2.4 Recommended Extras (not included) . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.5 The Microscope and its Components . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.5.1 Chamber1 ..................................... 7
2.5.2 Chamber2 ..................................... 8
2.5.3 SampleSpacer .................................. 8
2.5.4 Crown........................................ 9
2.5.5 PurgeValves .................................... 9
3 Installation and Use 10
3.1 ConnecttheHoloSeacable ................................ 10
3.2 Screwonlockingsleeve.................................. 11
3.3 EthernetConnection.................................... 11
3.4 TestingandDeployment.................................. 13
3.5 CollectingHolograms ................................... 13
3.5.1 Acquisition setup for Octopus and the microscope . . . . . . . . . . . . . . . 14
3.5.2 Tips for Optimal Hologram Acquisition . . . . . . . . . . . . . . . . . . . . . . 16
4 Care and Maintenance 16
5 Troubleshooting 18
6 Appendix 18
6.1 PrincipleofOperation ................................... 18
6.2 Software........................................... 19
7 Specifications 20
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LIST OF FIGURES
List of Figures
1 The preassembled HoloSea Microscope (vertical view in left panel and horizontal
viewinrightpanel). .................................... 4
2 10mCable ......................................... 4
3 PowerSupply(12VDC) .................................. 5
4 Carrying case, with the microscope inside . . . . . . . . . . . . . . . . . . . . . . . . 5
5 HoloSeacomponents ................................... 7
6 Protective sapphire camera window and copper ring. . . . . . . . . . . . . . . . . . . 8
7 Samplespace ....................................... 9
8 The two purge valves on the bottom of the microscope. . . . . . . . . . . . . . . . . 9
9 Mating the underwater connectors for a wet mating (Photo from MacArtney Under-
waterTechnologies) .................................... 10
10 HoloSea bulkhead with 13 pin connector. The male connector is in the left panel,
and is attached to the underwater cable. The female is shown in the right panel and
is attached to the microscope. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
11 Locking sleeve on both the cable (left panel), the microscope (center panel) and
connected(rightpanel) .................................. 11
12 Use of female to female Ethernet connector. In the right panel, the black cord is
the rigid Ethernet cable from the underwater cable, and the blue cable is the flexible
Ethernet cable to the computer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
13 Connectingtothecomputer................................ 12
14 Connecting the power. In the left panel connecting the microscope power to the in-
cluded 12VDC power cord. The right panel shows a close-up of the power connector
fromthemicroscope..................................... 12
15 Deployment of the HoloSea from a wharf . . . . . . . . . . . . . . . . . . . . . . . . 13
16 Dimensions of the Submersible, reported in inches . . . . . . . . . . . . . . . . . . . 13
17 Camera tab view (left panel) and the camera options (right panel) . . . . . . . . . . . 14
18 Select instrument preset dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
19 The Octopus software at start-up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
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HoloSea S7 1 OVERVIEW
1 Overview
The HoloSea has been developed to operate in conjunction with 4Deep’s software (Octopus,
Swordfish or Stingray). Note that hologram collection cannot be completed without the use of
4Deep software.
This user guide is strictly related to the installation, use, care of and functionality of the HoloSea.
For a detailed description of the setup and operation of the 4Deep software, please refer to the
respective user guides.
The HoloSea is a submersible holographic microscope; for the benchtop microscope, see the
Desktop Microscope.
The HoloSea can be used to collect images from the fields of:
• Marine research: water profiling, algae, plankton, phytoplankton
• Oil & gas
• Water quality and monitoring: microorganism imaging
• Ocean research
• Algae production: algae profiling
• Counting, data and morphological analysis, quantitative phase analysis: many other applica-
tions
1.1 Purpose
The HoloSea comes from a suite of instruments that all operate under proprietary digital inline
holography technology platform, developed by 4Deep. With its new and unique method of data
acquisition and analysis, this system is designed to optimize your research of the microscopic
world. The microscope is able to capture dynamic movement and is useful for time-dependent
experiments. The HoloSea allows you to quickly and easily observe micro-organisms and particles
up to a depth of 5 kilometres (in custom models).
The measurement technique used is digital inline holographic microscopy in transmission. The
light source is a single source of 405 nm.
1.2 Benefits
Compared to a traditional microscope, the holographic microscope has many benefits:
• Real-time, in-situ capability to observe of particles and micro-organisms in all aquatic envi-
ronments
• Portable and lightweight, making it easy to deploy, yet rugged
• High-flow capabilities; an be towed at 8 knots (4 m/s), or stationed in rivers
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2 INTRODUCTION HoloSea S7
• Low maintenance and easy to clean, as there is no pumps or tubing, making fouling less of
an issue
• Fast-tracking: up to 22 images per second to capture tracking dynamics of fast moving ob-
jects
• Save time using the fastest hologram image reconstruction available
• Go deeper, as it is pressure rated from 0-500m, with a cable depth of 100m, and Up to 6000
meters in custom models
• Instant: live imaging of samples without any manipulation.
• Simple: no need to focus.
2 Introduction
2.1 Safety Information
The user should read this user guide and any other additional information supplied by 4Deep before
operating the instrument.
This microscope contains a class IIIB Laser. A 405 nm wavelength is emitted from the
laser housing itself. If properly assembled, the light emitted from the laser should not pose any
threat of long term damage to an exposed eye. There are no user serviceable parts inside
the light source. If problems are encountered regarding the light source, please return it im-
mediately for service. Allow only a qualified technician to disassemble the point source. Do not
attempt to remedy any problems with the light source on your own!
Always make sure that the proper 12 VDC power supply is used with the microscope.
Failure to do so could result in critical damage to the microscope.
2.2 Compatibility
As mentioned above, the HoloSea needs to be used in conjunction with the Octopus software. The
computer requirements are:
• CPU Core i5 or i7
• 8 GB of RAM
• 256 GB or larger SSD Drive
–The microscope can record at 22 images per second, and each image is 4 MB
• NVIDIA GeForce or Quadro GPU with at least 2 GB of graphics RAM, Kepler architecture or
later
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HoloSea S7 2 INTRODUCTION
–For fast hologram reconstructions, 4Deep software requires a CUDA-enabled NVIDIA
graphics card to be installed in the computer
–For the list of CUDA-enabled graphics chips, refer to https://developer.nvidia.com/cuda-
gpus
• Gigabit Ethernet port (for data connection)
• 1 USB port for the HASP key -Full versions of the software require a valid HASP key (dongle)
to run
–Demo versions can be used without a HASP key
• Windows 7 or 10, 64-bit
–Windows 10 Pro is preferred over other versions (such as Home)
2.3 Components of the System
Be careful when unpacking the contents of the package. As the 4Deep microscope
images at the micron level, foreign objects (dust, dirt, fingerprints, smudges, perspiration, saliva
etc.) on the camera window and/or the point source can greatly affect the quality of the captured
holograms. Take care not to touch the sapphire panes encasing the camera and the point source.
For further Care and Cleaning information, see Section 4.
The following is the list of parts of the HoloSea.
• HoloSea, pre-assembled. For full details, see the microscope description in Section 2.5.
–There are two purge valves on the bottom of the microscope, as shown in the right panel
of Figure 1
– DO NOT REMOVE THE PURGE VALVES. Using the purge valve without
the advice of 4Deep WILL NEGATE ANY WARRANTY on the microscope. Purging of
the microscope MAY only be needed in one specific issue, thus in most cases, your
microscope will NOT need to be purged.
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2 INTRODUCTION HoloSea S7
Figure 1: The preassembled HoloSea Microscope (vertical view in left panel and horizontal view in
right panel).
• Long (10m) cable with 13 pin connector to power laser, camera, and transmit data from the
camera to the host computer.
Figure 2: 10m Cable
• Power supply (12 VDC)
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HoloSea S7 2 INTRODUCTION
Figure 3: Power Supply (12 VDC)
• Carrying case
Figure 4: Carrying case, with the microscope inside
Please ensure all components listed above were shipped to you. If not, please contact
a 4Deep representative immediately.
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2 INTRODUCTION HoloSea S7
2.4 Recommended Extras (not included)
The following is a list of recommended extra components, suggested by 4Deep, to optimize the
use of your 4Deep HoloSea. Note that none of these are necessary for the use of the HoloSea
and the HoloSea is fully functional without.
• Molykote 44 Medium, for marrying the connectors (Subsection 3.1)
• Deployment rope/cord, to deploy the HoloSea (Section 3.4)
• A female-female Ethernet connector (ex: from a computer hardware store, shown in Figure
12)
• Lint-free wipes/swabs (ex: Kim-tech), for use in cleaning (Section 4)
• Glass/window cleaner, for use in cleaning (Section 4)
2.5 The Microscope and its Components
The HoloSea consists of 5 primary components:
1. Chamber 1: houses the laser point source
2. Chamber 2: houses the camera
3. Sample Space: connects the two chambers, determines the sample volume that will be
imaged.
4. Crown
5. Purge Valves
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HoloSea S7 2 INTRODUCTION
Figure 5: HoloSea components
2.5.1 Chamber 1
This Chamber contains a digital camera. The camera’s image sensor is protected by a sapphire
glass window. The sapphire window also has a copper ring around it, to reduce the effect of
biofouling on the instrument (shown in Figure 6).
This window is the most fragile external component of the microscope, and must be
handled carefully.
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2 INTRODUCTION HoloSea S7
Figure 6: Protective sapphire camera window and copper ring.
Be careful when handling the microscope. At the micron level, smudges on the windows
can greatly affect the quality of the captured holograms. Take care not to smudge the windows.
2.5.2 Chamber 2
This Chamber contains the laser point source, consisting of a 405 nm laser and a fibre optic cable,
which serves as a point source. The point source provides the spherical wave of light necessary
to produce images in inline holography. Similar to the camera in Chamber 1, the point source is
protected by a sapphire glass window (see previous paragraph for care instructions).
2.5.3 Sample Spacer
The Sample Spacer provides a stable environment for imaging microorganisms and particles in
addition to determining the source to screen distance of the instrument, which is essential for
proper data analysis.
The Sample Space, determined by the Sample Spacer, allows for the non-destructive flow of or-
ganisms and particles. The HoloSea’s camera collects holograms of the samples as they, along
with the fluid which contains them, pass through the Sample Space. The standard Sample Space
for a HoloSea is 15 mm.
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HoloSea S7 2 INTRODUCTION
Figure 7: Sample space
2.5.4 Crown
The Crown is the metal framing around the connector on the HoloSea. Its main purpose is for
handling and deployment.
2.5.5 Purge Valves
There are two purge valves on the bottom of the microscope, as shown in the right panel of Figure
8.
Figure 8: The two purge valves on the bottom of the microscope.
The purge valves do not need to be used to ensure the microscope operates correctly. If a 4Deep
representative deems it necessary for the purge valves to be opened, it will be completed at the
4Deep office, NOT BY THE USER. Note that using the purge valves is only necessary to solve
one issue that MAY occur with the microscope, so it is likely the purging will not need to occur.
DO NOT USE THE PURGE VALVES. Using the purge valve without the advice of 4Deep
WILL NEGATE ANY WARRANTY on the microscope.
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3 INSTALLATION AND USE HoloSea S7
3 Installation and Use
3.1 Connect the HoloSea cable
Firstly, ensure the connector pins (male and female) are clean, and free of any dirt/dust before
connecting.
The connector pin manufacturer suggests using Molykote 44 Medium grease before every mat-
ing (Figure 9). The manufacturer suggests greasing about 1/3 of the female socket depth (right
panel of Figure 9), for a “wet mating” (ie if the connector/microscope is being submerged). The
manufacturer suggests greasing about 1/10 of the female socket depth , for a “dry mating” (ie if
the connector/microscope is not being submerged, for example, when using the microscope in a
laboratory environment).
Figure 9: Mating the underwater connectors for a wet mating (Photo from MacArtney Underwater
Technologies)
As you push the connectors together, take care not to wiggle the cable too much, as it
may cause damage the pins.
Firmly push the 13 pin connector at the end of the main underwater cable into the bulkhead con-
nector. Push the cable connector all the way in. To verify that all of the male connectors are
greased, pull the connectors apart, and check that the male pins are all coated in grease. Then
reconnect the cable.
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HoloSea S7 3 INSTALLATION AND USE
Figure 10: HoloSea bulkhead with 13 pin connector. The male connector is in the left panel, and
is attached to the underwater cable. The female is shown in the right panel and is attached to the
microscope.
3.2 Screw on locking sleeve
Slide the locking sleeve over the cable connectors and screw it onto the bulkhead connector.
Figure 11: Locking sleeve on both the cable (left panel), the microscope (center panel) and con-
nected (right panel)
3.3 Ethernet Connection
It is highly recommended that you use a flexible Ethernet cable, and a female-female
Ethernet connector as the underwater cable is very rigid and may damage the Ethernet port on
your computer.
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3 INSTALLATION AND USE HoloSea S7
Figure 12: Use of female to female Ethernet connector. In the right panel, the black cord is the
rigid Ethernet cable from the underwater cable, and the blue cable is the flexible Ethernet cable to
the computer.
• Connect the Ethernet end of the main cable to the Ethernet port on the computer.
Figure 13: Connecting to the computer
• Plug in the power adapter for the camera and plug in the laser power adapter to the connector
on the same cable.
Figure 14: Connecting the power. In the left panel connecting the microscope power to the included
12VDC power cord. The right panel shows a close-up of the power connector from the microscope.
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HoloSea S7 3 INSTALLATION AND USE
3.4 Testing and Deployment
Many applications of the HoloSea will require deploying the HoloSea into a body of water (river,
ocean, etc.) off a platform (boat, wharf, etc.).
DO NOT deploy the HoloSea with the underwater cable alone. Attach a rope to the
crown atop the HoloSea for deployment. Submerse the microscope into the body of water/fluid that
you want to look at. Both sapphire windows should be fully submersed in water for the accurate
imaging to be performed.
Figure 15: Deployment of the HoloSea from a wharf
More complex deployment methods may also be necessary, as researchers may wish to deploy
the HoloSea in conjunction with other instruments. As this would be application-specific, we leave
the details of the deployment up to the user, but give the dimensions of the HoloSea system for
technical purposes:
Figure 16: Dimensions of the Submersible, reported in inches
3.5 Collecting Holograms
To collect holograms, it is important to setup both the microscope and Octopus (4Deep’s software)
properly. The steps below detail how to setup and use Octopus in conjunction with a 4Deep
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3 INSTALLATION AND USE HoloSea S7
microscope. Note that you should be using both this user guide, as well as the user guide for
Octopus for complete setup. You will also notice that much of the information listed below is also
listed in the Octopus User Guide.
3.5.1 Acquisition setup for Octopus and the microscope
• Ensure that the point source and camera are clean, free of dust, smudges, etc., as the
presence of dust/dirt can greatly affect the quality of holograms, especially at the micron
level.
• Start Octopus and click on the Camera Tab to connect Octopus to the camera (see Octopus
User Guide for more details) .
–If camera is not connected, check that the camera cables are properly attached, and
power is on. Click Connect to Camera button to retry the connection. Note: it may take
several seconds to connect to the camera. For more help on connecting the camera,
see the Troubleshooting Guide (Section 5).
–The live view from the camera appear in the preview and hologram reconstructions will
be performed in real time at the rate of up to 16 frames per second. Higher frame
rates are possible with reduced image sizes (ex: 50 fps for 1024x1024 pixels). All
reconstruction parameters can be applied to the real time reconstructions, including the
reconstruction position and mode.
Figure 17: Camera tab view (left panel) and the camera options (right panel)
• Click the “View” button to start viewing (but not recording) the feed
• To properly reconstruct holograms, settings including the source-to-screen distance need to
be added to Octopus.
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HoloSea S7 3 INSTALLATION AND USE
–Select the Preset Option for the HoloSea: Settings -> Reconstruction Options-> Preset.
Figure 18: Select instrument preset dialog
Go to Octopus User Guide for further details on capturing holograms (Section 4 in the
Octopus User Guide).
Figure 19: The Octopus software at start-up
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