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User's
Manual
Confocal Quantitative Image Cytometer
The translation of the original instructions
~However warning labels are not the same.~
Yokogawa Electric Corporation
IM 80J01A01-01E
IM 80J01A01-01E
10
Edition
th

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Summary of Contents for YOKOGAWA CQ1

  • Page 1 User’s Manual Confocal Quantitative Image Cytometer IM 80J01A01-01E The translation of the original instructions ~However warning labels are not the same.~ IM 80J01A01-01E Yokogawa Electric Corporation Edition...
  • Page 2 This document corresponds to the following versions of software Measurement software R1.04...
  • Page 3 This manual describes the functions, installation and wiring procedures, operating procedures and handling precautions of the CQ1. Before you start to use the CQ1, please read this manual carefully to enable correct use of the system. After reading this manual, keep it in a handy place so that you can refer to it whenever necessary.
  • Page 4 For Safe Use of This Equipment To ensure safe and correct use of this equipment, be sure to follow the precautions below when using this equipment. If this equipment is used in a manner not specified in this manual, the protection provided by this equipment may be impaired.
  • Page 5 Following warning labels are attached on this equipment. Warning label (1) This warning label indicates that the operator must refer to the instruction manual to prevent injury and/or damages on the instrument. Warning label (2) This warning label indicates that this is laser product and operator must prevent injury and/or damages of skin or eyes from laser exposure.
  • Page 6 Location of Warning Labels ●Right Side of Main Unit Warning label (3) Warning label (3) Explanation label (1) ●Rear Panel of Main Unit Warning label (3) ●Top Panel of Main Unit Warning label (4) IM 80J01A01-01E...
  • Page 7 ●Rear Panel of Main Unit (Transmission Illumination Option) Warning label (3) Warning label (3) ●Front Panel of Utility Box Warning label (2) Warning label (1) ●Rear Panel of Utility Box Warning label (1) Explanation label (2) IM 80J01A01-01E...
  • Page 8 ●Right Side of Utility Box Aperture label IM 80J01A01-01E...
  • Page 9 3%, it may be harmful to the human body. Be sure to provide ventilation, lead exhaust gas from CQ1 to outside of the room, or take other appropriate measures. It is also recommended that an alarm system be installed in case of emergency.
  • Page 10 viii CAUTION  Use the I/O terminals of the equipment within the ranges of the specifications to prevent damage to the equipment.  This product uses precision optics. Therefore, do not use the equipment in locations where there are large vibrations, a lot of dust, high humidity and high temperature (in places near heating equipment or exposed to direct sunlight), rapid changes in the temperature (in places subject to dew condensation), or corrosive...
  • Page 11 Laser Products Handling Precautions  Laser products are classified according to their exposure emission limit determined by the wavelength and power characteristics of laser beam. A different set of common safety standards applies to each class of products. The product explained herein belongs to Class 1.
  • Page 12 “Warranty Rule.”  Yokogawa shall assume no responsibility for any loss suffered by a customer or third party as a result of use of this product, or any loss or indirect loss suffered by a customer or third party due to a defect in this product or any other problem not predictable by Yokogawa.
  • Page 13 CQ1 Main Unit Communication cable to connect CQ1 main unit and workstation USB cable Power supply and communication cable to connect CQ1 main unit and utility box Main Unit⇔UTB cable Equipment for supply power and excitation laser light Utility Box...
  • Page 14 Remote interlock connector on Utility Box Remote Interlock Objective Lens Part Quantity Description To be installed on CQ1 main unit One to six lenses are installable depending on the specification. 1~6 Please refer to Parts List: CMPL 80J01A01-01 for details.
  • Page 15 Transmission Illumination Supply mixture gas that O concentration is contolled to stage attachment Gas mixer (TOKAI HIT, GM-8000) Tube to connect CQ1 main unit and Gas mixer Attached if stage heater option is selected Gas mixer connecting tube Stage attachment that all wells of...
  • Page 16 Option (Sold separately, continue from previous page) Part Quantity Description Stage attachment which can keep the temperature, O concentration and humidity constant Stage attachment (Chambered type) Sample holder for set three 35 mm dishes Sample holder for triple 35 mm dishes Sample holder for set one 60 mm dish Sample holder for...
  • Page 17 Sample holders are set into the stage attachment as shown below. Sample Sample holder Stage attachment XY stage IM 80J01A01-01E...
  • Page 18 How to use this manual This user manual consists of Chapters 1 to 9, the details of which are explained below. Chapter Title and Content Function Overview A functional overview of this equipment is explained. Before Use Precautions for use and installation/wiring methods are explained. Name of Each Part/Starting and Shutting Down the Equipment The name of each part and starting/shutdown of the equipment are explained.
  • Page 19: Table Of Contents

    Name of Each Part/Starting and Shutting Down the Equipment ....3-1 Name and Function of Each Part ..............3-1 Starting and Shutting Down of CQ1 ............... 3-8 Starting and Shutting Down of Gas Mixer (Option) ......3-13 Measurement Procedures ......4-1 Measurement Procedures ..................
  • Page 20 Functions of CQ1 Software ......5-1 Outline ..........................5-1 Main Menu ......................... 5-3 Operation Mode Panel ....................5-8 Control Panel (CQ Mode) ..................5-10 Control Panel (HDD Mode) .................. 5-56 Viewer ..........................5-80 Status Panel ........................ 5-122 Viewer Layout ......................5-123 Channel Setting......................
  • Page 21: Function Overview

    Different from flow cytometetric analysis in which cells are washed away, CQ1 measures the cells in their culture vessels such as microplate, thus it is possible to analyze the same cells repeatedly or follow their temporal changes.
  • Page 22 <1. Function Overview> Measurement values CQ1 outputs the following measurement values by analyzing confocal images of fluorescently labelled each cell. Measurement Unit Measurement Description Method Morphological Area µm Measure the area of objects. features measurement Circumference µm Measure the circumference of object.
  • Page 23: Principle Of The Nipkow Disk System With Micro-Lens

    <1. Function Overview> 1.2 Principle of the Nipkow Disk System with Micro-lens Two disks, including the “pinhole array disk” having many pinholes arranged in a helical pattern, and the “Micro-lens array disk” that condenses excitation laser to individual pinholes, are rotated jointly at high speed to perform multiple scans over the observation area with approximately 1,000 laser beams.
  • Page 25: Precautions For Use/Installation

    Workstation for performance improvement. Therefore, the third-party software may not work normally.  Do not install any third-party hardware to CQ1 Main Unit, Utility Box, and Workstation. The third-party hardware may fail.  In case of connecting Workstation to Internet, please install an antivirus program which your affiliated facilitate designated and perform virus check periodically.Please don’t perform virus check...
  • Page 26: Installing The Equipment

    Install this equipment in a location meeting the conditions specified below. Please call service personnel when you install or move the equipment. Installation example 1) In case of using CQ1 normal gas mixer. Note Please prepare following gas cylinder and regulator Gas cylinder...
  • Page 27 <2. Precautions for Use/Installation> Installation example 2) In case of using gas mixer that user prepares. IM 80J01A01-01E...
  • Page 28 ※ changes.  Location of minimal mechanical vibration Never set any vibrating devices, such as centrifuge or mixer, on the same table with CQ1. Doing so may disrupt optical performance. IM 80J01A01-01E...
  • Page 29 Subjecting the equipment to a sudden temperature shift may cause condensation. Installation Environment  Operating Temperature Range CQ1: 15 – 35 ℃ Gas Mixer: 20 – 35 ℃  Operating Humidity Range CQ1: 20 – 70 % RH, non-condensing Gas Mixer: 10 – 85 % RH, non-condensing IM 80J01A01-01E...
  • Page 30: Wiring The Peripherals

    <2. Precautions for Use/Installation> 2.3 Wiring the Peripherals Connect the cables after confirming that the power switch on the equipment is turned off. CAUTION Please don’t connect any cables other than specified by YOKOGAWA. CQ1Main Unit Workstation USB Cable Display...
  • Page 31: Connecting The Power

    CAUTION Please refrain from applying the following processing on the CQ1 workstation. If you do, there is a risk of malfunction of this instrument. In case, any problems happened as a result of such inappropriate processing, you are liable for the cost of repair.
  • Page 32 Power cable and plug To prevent electric shock and fire, use the power cable supplied by Yokogawa. For the main power plug, only use a power socket with a protective grounding terminal. Use of an extension cable without protective grounding wire will disable the protective operations ...
  • Page 33 <2. Precautions for Use/Installation>  Removal of the case The case must not be removed except by Yokogawa’s service personnel. Some parts in this equipment carry high voltage and a Class 3B laser is also housed inside. Accordingly, removing the case presents dangerous situations.
  • Page 35: Name Of Each Part/Starting And Shutting Down The Equipment

    <3. Name of Each Part/Starting and Shutting Down the Equipment> 3 Name of Each Part/Starting and Shutting Down the Equipment 3.1 Name and Function of Each Part CQ1 Main Unit (1) Door Door opens/closes either manually by the door button, or through the software; [CQ]button→[Sample]tab→[Sample Loader]→...
  • Page 36 (13) (14) (12) (9) Fiber Port Port to connect the fiber to CQ1 Main Unit (10) USB Connector Connector for USB cable connection with the Workstation cable (11) Gas Inlet Port Port to connect the tube from Gas Mixer (option)
  • Page 37 <3. Name of Each Part/Starting and Shutting Down the Equipment> Transmission Illumination (1) Switching lever (bright field/ phase contrast) Switch the method of transmission illumination. Pull the lever toward to switch to bright field. Push the lever back to switch to phase contrast.
  • Page 38 (6) EMISSION Lamp Lights when laser emits, and lights out when laser is off (7) Power Switch Switch ON to power on CQ1 Main Unit Switch OFF to power off CQ1 Main Unit IM 80J01A01-01E...
  • Page 39 (11) Remote Interlock Connector Port to connect lase interlock connector (12) Reserved Connector Not in use (13) CQ1 Main Unit Power Cable Connector Port to connect power cable (14) Fiber Port Port to insert the fiber to Utility Box IM 80J01A01-01E...
  • Page 40 (6) 100 % N Port to connect the tube from N gas cylinder via the regulator (7) Mix Gas OUT Port to connect the tube to CQ1 Main Unit (8) GM LINK Not in use (9) DC IN Port to connect cable of attached AC adapter...
  • Page 41 <3. Name of Each Part/Starting and Shutting Down the Equipment> Workstation (1) USB Connector Connect to the USB connector (8) on the CQ1 Main Unit. Connect supplied cable as shown above. (2) Camera Link Cable Connector Connect camera link cable out of CQ1 Main Unit as shown above.
  • Page 42: Starting And Shutting Down Of Cq1

    (2) Power ON the Workstation. (3) Confirm that there is enough free space in data (D:) disk drive. Data volume of one image that CQ1 outputs is about 11MB. Keep free space in data (D:) disk drive by considering total image quantity to acquire.
  • Page 43 <3. Name of Each Part/Starting and Shutting Down the Equipment> (4) Wait until Ready lamp on Utility Box turn ON after blinking. (It takes about 1 minute from turning the key switch on). Click the desktop icon of the Workstation to start CQ1 Software. READY lamp IM 80J01A01-01E...
  • Page 44 <3. Name of Each Part/Starting and Shutting Down the Equipment > 3.2.2 Shutting Down CQ1 (1) Select [File] menu → [Exit] menu, or click the close box on the main screen of CQ1 Software window. close box (2) Click [OK] button.
  • Page 45 3-11 <3. Name of Each Part/Starting and Shutting Down the Equipment> (3) Shut down Workstation. (4) Turn the key switch on the Utility Box to OFF. (5) Turn the key switch OFF, then turn the power switch OFF.. Power Switch Key Switch IM 80J01A01-01E...
  • Page 46 3-12 <3. Name of Each Part/Starting and Shutting Down the Equipment > 3.2.3 Offline Mode You can start CQ1 Software by “offline mode” without turning equipment on. It is convenient for viewing data or analyzing without measurement. Starting procedure is different from above. Select”CQ1 Offline” from Windows start menu.
  • Page 47: Starting And Shutting Down Of Gas Mixer (Option)

    3-13 <3. Name of Each Part/Starting and Shutting Down the Equipment> 3.3 Starting and Shutting Down of Gas Mixer (Option) 3.3.1 Starting Gas Mixer Power Switch Meter B Meter A ① ③ ② (1) Confirm that valve ③ of regulator is closed. (2) Confirm that valve ②...
  • Page 49: Measurement Procedures

    <4. Measurement Procedures> 4 Measurement Procedures 4.1 Measurement Procedures Turn the power switch ON, then turn the key switch ON.. Power Switch Key Switch CAUTION Immediately pull out the AC cord from inlet of equipment, when you notice smoke coming out of the main unit, foul smell, abnormal noise or any other abnormality.
  • Page 50 <4. Measurement Procedures> <In case of exchanging All Well Imaging Type to Chambered Type> Click “Sample” tab → “OPEN” Button of CQ1 Software or do long press (3 seconds) of Door OPEN/CLOSE Button of CQ1 Main Unit to open the door.
  • Page 51 <4. Measurement Procedures> Push lever and lift up to remove Stage Attachment. Lever CAUTION Lift up Stage Attachment vertically because it is positioned by pin. Be careful not to collide with cover. IM 80J01A01-01E...
  • Page 52 <4. Measurement Procedures> Prepare Stage Attachment to set. Direct clamp as following diagram and set Stage Attachment. Be careful not to collide with cover. Clamp Put Stage Attachment on the stage and set it with pushing lever. Lever IM 80J01A01-01E...
  • Page 53 <4. Measurement Procedures> CAUTION Be careful not to touch sample setting part of Chambered Type Stage Attachment when put it on the stage. This part is easily-broken. Sample setting part Fasten 2 screws. CAUTION Confirm that Stage Attachment does not tilt. Stage Attachment Stage IM 80J01A01-01E...
  • Page 54 <4. Measurement Procedures> Set Sealing Block for Clamp on the clamp. In case of using microplate, set Sealing Block for Microplate as following diagram. IM 80J01A01-01E...
  • Page 55 <4. Measurement Procedures> Turn the power switch ON, then turn the key switch ON.. CAUTION After turning power switch ON, the door closes automatically. Please be careful not to pinch your fingers or others. Immediately pull out the AC cord from inlet of equipment, when you notice smoke coming out of the main unit, foul smell, abnormal noise or any other abnormality.
  • Page 56 <4. Measurement Procedures> <In case of exchanging Chambered Type to All Well Imaging Type> Click “Sample” tab → “OPEN” Button of CQ1 Software or do long press (3 seconds) of Door OPEN/CLOSE Button of CQ1 Main Unit to open the door.
  • Page 57 <4. Measurement Procedures> Remove Sealing Block for Clamp. Exchange Stage Attachment referring to page 4-1. CAUTION Be careful not to touch sample setting part of Chambered Type Stage Attachment when remove it from the stage. This part is easily-broken. Sample setting part IM 80J01A01-01E...
  • Page 58 4-10 <4. Measurement Procedures> Turn the power switch ON, then turn the key switch ON.. CAUTION After turning power switch ON, the door closes automatically. Please be careful not to pinch your fingers or others. Immediately pull out the AC cord from inlet of equipment, when you notice smoke coming out of the main unit, foul smell, abnormal noise or any other abnormality.
  • Page 59 4.1.5 Setting Samples. In case that measurement is running, click “Pause” button to pause. Click “Sample” tab → “OPEN” Button of CQ1 Software or do long press (3 seconds) of Door OPEN/CLOSE Button of CQ1 Main Unit to open the door.
  • Page 60 During temperature controlling, water drops are formed on the downside of the bath cover. Please be careful not to drop water inside the equipment when removing bath cover. If water drops inside the equipment, wipe it completely before turning CQ1 on. Water drop IM 80J01A01-01E...
  • Page 61 4-13 <4. Measurement Procedures> If the waterbath is empty, pour 25 ml of distilled water. (It is recommended to pour by syringe.) Pour distilled water to cover whole area of the bath. IM 80J01A01-01E...
  • Page 62 4-14 <4. Measurement Procedures> CAUTION It is acceptable that the bath is not filled with water. If too much water is poured, it causes water immersion into the equipment and failure of the equipment. Note Appropriate humidity level is maintained over 6 hours when 25 ml of water is poured.
  • Page 63 4-15 <4. Measurement Procedures> Set bath cover and tighten 4 screws. In case that the screws can’t be fastened properly, adjust position of bath cover so that the screws are fastened properly. Set sub cover and tighten 2 screws. Turn the power switch ON, then turn the key switch ON.. Power Switch Key Switch CAUTION...
  • Page 64 4-16 <4. Measurement Procedures> Click “Rec” button in case of restarting measurement. (It takes about 2 minutes that “Rec” button becomes available after turning power switch ON.) Note In case that starting time of the next timepoint comes during the pausing time, measurement starts again as following sequence.
  • Page 65 4-17 <4. Measurement Procedures> 4.1.3 Procedures of Setting Gas Mixer This procedure is only perfomed when controlling environment around sample. If you don’t need environment control, go to procedure shown 4.1.5 Setting Samples. Start Gas Mixer by referring to 3.3 Starting and Shutting Down of Gas Mixer (Option).
  • Page 66 4-18 <4. Measurement Procedures> 4.1.4 Procedures of Setting Stage Heater This procedure is only perfomed when controlling environment around sample. If you don’t perform environment control, go to procedure shown in 4.1.5 Setting Samples. Click “ON” button in “Environment” window -> “Temperature Control”. Click “Edit”...
  • Page 67 4-19 <4. Measurement Procedures> It changes to temperature setting window. Input control temperature to “Setting” and click “Set”. Guarranty range of chamber temperature depends on room temperature (refer to following chart). For example, to set chamber temperature 37 ℃, set room temperature 20 ℃...
  • Page 68 <Caution when setting samples> If the sample which is taken from cold environment, such as refrigerator, is set into CQ1 at once, condensation occurs on the bottom of sample vessel and autofocus may not operate normally. Also, temperature of sample vessel changes rapidly after it is set into CQ1, strain of sample vessel occurs and autofocus may not operate normally.
  • Page 69 4-21 <4. Measurement Procedures> <In case of using 35 mm dish> Set dishes on sample holder. Sample holder for 35 mm dishes Lift up leaf spring, set a dish, and push down leaf spring to fix a dish. Lift up leaf spring Set a dish and push down leaf spring to fix a dish.
  • Page 70 4-22 <4. Measurement Procedures> <In case of using 60 mm dish> (Only when controlling environment) Set rubber on the dish. Set dish on sample holder. (Only when controlling environment) Set a dish ring. Dish ring IM 80J01A01-01E...
  • Page 71 4-23 <4. Measurement Procedures> Fix a dish by leaf spring. Lift up leaf spring Set a dish and push down leaf spring to fix a dish In case of performing environment control In case of not performing environment control IM 80J01A01-01E...
  • Page 72 Set a slide on sample holder with pressing to leaf spring. Please be careful not to tilt slides. Set a slide with pressing to leaf spring. Please set slides such as label comes near side basically (depend on the slide glass setting in CQ1 Software; refer to page 5-19) IM 80J01A01-01E...
  • Page 73 4-25 <4. Measurement Procedures> CAUTION  Set slides not to put cover glass on sample holder. Sample holder Slide glass Cover glass × IM 80J01A01-01E...
  • Page 74 4-26 <4. Measurement Procedures> <In case of using cover glass chamber> (Only when controlling environment) Remove rid from cover glass chamber, set rubber on the cover glass chamber fastly and set rid again. Rubber list For IWAKI (2 holes) For NUNC Lab-Tec I (3 holes) For NUNC Lab-Tec II For MATSUNAMI (5 holes)
  • Page 75 4-27 <4. Measurement Procedures> (Only when controlling environment) Set a holding plate. Holding plate Fix a cover glass chamber by leaf spring. Set a cover glass chamber and push down leaf spring to fix In case of performing environment control In case of not performing environment control IM 80J01A01-01E...
  • Page 76 4-28 <4. Measurement Procedures> <Common procedures> Click “Sample” tab → “Open” Button of CQ1 Software or do long press (3 seconds) of Door OPEN/CLOSE Button of CQ1 Main Unit, set microplate or sample holder on stage. Click “Close” Button of CQ1 Software or do long press (3 seconds) of Door OPEN/CLOSE Button of CQ1 Main Unit to close the door.
  • Page 77 4-29 <4. Measurement Procedures> In case of using sample holder, set it in CQ1 as projection portion faces left-side of CQ1. Projection Portion Projection Portion CAUTION If you don’t set microplate or sample holder properly, it may result to equipment damage. Please confirm that 4 corners of the microplate or sample holder are set on stage and it is moved lightly (not to be stuck to edge of sample setting place).
  • Page 78 4-30 <4. Measurement Procedures> If you perform measurement by protocol which has been made, go to procedure shown in 4.8 Sample Measurement. IM 80J01A01-01E...
  • Page 79: Basic Protocol Setting

    4-31 <4. Measurement Procedures> 4.2 Basic Protocol Setting Designate the folder for saving the measurement data in “Protocol” window. ※ Designate parent folder Input suffix of folder name Input description if needed ※ Note Please designate local drive (D:) as data storage folder. In case of designating other than local drive (D:), performance of HDD decreases, and it may cause errors during image acquisition.
  • Page 80 4-32 <4. Measurement Procedures> Switch to “Imaging” window. Double click imaging channel setting part to open “Channel Setting”. Set the lasers and emission filters for each imaging channel. (For details, refer to 5.9 Channel Setting) Double click IM 80J01A01-01E...
  • Page 81: Sample Searching

    4-33 <4. Measurement Procedures> 4.3 Sample Searching Search the position that samples exist (suitable position to imaging) by low magnification objective lens. Set the viewer layout to “Image & Map”. In “Imaging” window, select imaging channel, well and objective lens. For sample searching, use low magnification objective lens (2x –...
  • Page 82 4-34 <4. Measurement Procedures> In “Z stack” of “Imaging” window (refer to page 5-28), click “Search” to search Z position which samples exist. After Z position search, click “<<” to apply the result of searching to Z Stack parameter. Apply the result of searching to Z Stack parameter.
  • Page 83 4-35 <4. Measurement Procedures> Note Blue region in “Map” window can’t be designated as imaging region because objective lens interferes with stage attachment, sample holder and sample vessel. After map imaging, select “Test imaging mode” (refer to page 5-94), change objective lens to that for measurement, and select suitable field for measurement.
  • Page 84: Imaging Setting

    4-36 <4. Measurement Procedures> 4.4 Imaging Setting If needed, perform following (1) – (3) setting. (1) Imaging channel setting “Channels” window of “Imaging” window (refer to page 5-22), change “Excitation Power” and/or “Exposure” of each imaging channel. Select imaging channel Change “Excitation Power”...
  • Page 85 4-37 <4. Measurement Procedures> (2) Autofocus and 2D/ 3D imaging setting In “Z Stack” window of “Imaging” window (refer to page 5-28), change autofocus setting. Change “Range” and “Slices”. As well, set 1 to “Slices” and 2D measurement is executed. Set 2 or more and 3D measurement is executed.
  • Page 86 4-38 <4. Measurement Procedures> <About CQ1 autofocus> CQ1 can perform 2 types of autofocus, which are laser based and image based. Laser Autofocus detects surface of bottom plate or cover glass by laser and set the surface as Z base position. Please note that surface to detect (Z base positon) is different by the kind of sample vessel.
  • Page 87: Analysis Protocol Setting

    4-39 <4. Measurement Procedures> 4.5 Analysis Protocol Setting Set the viewer layout to “ImageViewer & Chart”. Pre-acquire the images for analysis setting. In “Wells” window of “Imaging” window (refer to page 5-25), make ① button to status (green) , select a few wells from wells for measure ※...
  • Page 88 Select “Application” tab if you use analysis protocol which is preloaded in CQ1 Software (Cell Cycle, FISH and so on). Select “Template” tab if you use basic protocol which is preloaded in CQ1 Software. Select analysis protocol and click “Load” to load analysis protocol.
  • Page 89 4-41 <4. Measurement Procedures> If needed, in “Object Detect Setting” window of “Application” window (refer to page 5-44), change setting of object recognizing of each imaging channel. If needed, in “Link Setting” window of “Application” window (refer to page 5-46), change link setting between each object. IM 80J01A01-01E...
  • Page 90: Object Recognizing Condition Setting

    4-42 <4. Measurement Procedures> 4.6 Object Recognizing Condition Setting In “Analysis” window, click “Single Preview” (single object) or “Preview” (all objects) to confirm result of object recognizing. If it is necessary to improve the result, adjust recognizing condition as following. If it is necessary to improve more, click “Edit”, open “Advanced Editor”...
  • Page 91: Protocol Saving

    4-43 <4. Measurement Procedures> In “Wells” window of “Analysis” window (refer to page 5-51), make ① button to status (green), select wells which were executed “PreRec” above procedure (selected wells become pink), and click “PreAnalyze”. Confirm that objects are detected properly in multiple wells. If it is necessary to improve the result, adjust detecting condition in the field which object isn’t detected properly.
  • Page 92 4-44 <4. Measurement Procedures> Select “Protocol” tab and click “Save As”. Input name and descriptions of the protocol. Click “Save” to save the protocol. IM 80J01A01-01E...
  • Page 93: Sample Measurement

    4-45 <4. Measurement Procedures> 4.8 Sample Measurement In case of measurement by saved protocol, select protocol from “Protocol” window. Note In case of measuring other sample in same protocol again, please load the protocol in each time. If the protocol is not loaded, autofocus may not operate normally. ①...
  • Page 94 4-46 <4. Measurement Procedures> In case of pausing measurement, click “Pause” button. In case of re-starting measurement during pausing, click “Stop” button. In case of stopping, click “Stop” button. Stop button Acquired images are displayed in “ImageViewer” and statistic of feature data (default is “Count”) of wells which measurement is finished are displayed in “WellTable”...
  • Page 95 4-47 <4. Measurement Procedures> (white) and select well in “WellTable”. Make ① button to status Acquired images and result of recognition are displayed in “ImageViewer”. Make ① button to status (green), check number of Thumbnail Chart to display and select wells in “WellTable”. Scattergrams or histograms are displayed in “ThumbnailChart”.
  • Page 96 4.6 Object Recognizing Condition Setting, and click “Analyze” In case of stopping analysis process, click “Stop” button. Output acquired images, window snapshot of CQ1 Software or CSV data and so on in “Output” window. (For details, refer to 5.5.4 Output Window.)
  • Page 97: Outline

    <5. Functions of CQ1 Software> 5 Functions of CQ1 Software 5.1 Outline CQ1 Software is the application software to control both CQ1 Main Unit and Utility Box and runs sample measurement. There are two operating modes; CQ mode and HDD mode, and the window display changes depending on the mode.
  • Page 98 <5. Functions of CQ1 Software> (2) HDD Mode This mode is to view measurement data or to retry image analysis under modified analysis conditions. In HDD mode, it is able to output data for report such as screen shot, movie, feature data and so on.
  • Page 99: Main Menu

    <5. Functions of CQ1 Software> 5.2 Main Menu 5.2.1 File Menu (1) Save Measurement Protocol as Default Save the default measurement condition file. Its channel setting and analysis conditions shall be applied at the next start. (2) Save as Measurement Protocol Save the current measurement condition file.
  • Page 100 <5. Functions of CQ1 Software> (3) Load Measurement Protocol Load measurement condition fle designated by file read-in dialog. In CQ mode, conditions such as objective lens, sample vessel, Z stack, Fields to be imaged and analysis conditions are applied. Fields to be imaged aren’t applied if stage attachment and sample holder isn’t matched.
  • Page 101 (3) User Setting Open User Setting window to change user setting. Please refer to “5.11 User Setting” for details. (4) Activation Setting Open Activation Setting window to manage license of CQ1 “5.12 Activation Software. Please refer to Setting” for details. CAUTION Please do not operate Activation Setting window except when necessary such as updating CQ1 Software.
  • Page 102 (5) Run as External Control Following “Robot Service Hosting” window opens and changes to the external control mode that high-order computer controls CQ1. Select this menu in case of operating CQ1 with external robot. Click “Cancel” to quit external control. 5.2.3 View Menu Viewers corresponding to each menu item are shown.
  • Page 103 <5. Functions of CQ1 Software> 5.2.4 Help Menu (1) About CQ1 Version information is shown. (2) Make System Analysis Report Collect system analysis information and output a compressed file of log and calibration file under CVSysRep folder on desktop. The output data will be used for system maintenance service when error occures.
  • Page 104: Operation Mode Panel

    Highlighted in the CQ mode but nothing happens by clicking this button. (Refer to 5.1 Outline (1) CQ Mode) (3) HDD Mode Button Click to shift CQ1 Software to HDD mode. Cannot click it during measurement. (Refer to 5.1 Outline (2) HDD Mode) (4) Rec Button Click to start measurement after setting measurement conditions on the control panel.
  • Page 105 : Click to HIDE control panel display : Click to SHOW control panel display (2) CQ Mode Button Click to shift CQ1 Software to CQ mode. Cannot click it during analyzing measurement data. (Refer to 5.1 Outline (1) CQ Mode)
  • Page 106: Control Panel (Cq Mode)

    5-10 <5. Functions of CQ1 Software> 5.4 Control Panel (CQ Mode) In CQ mode, click left-side tabs to set measurement conditions and so IM 80J01A01-01E...
  • Page 107 5-11 <5. Functions of CQ1 Software> 5.4.1 Protocol Window Protocol means sample measurement conditions such as imaging conditions specified at “Imaging window”, and analysis conditions specified at “Application window” and “Analysis window”. “Protocol window” is to save or load Protocol, and specify the folder name to save measurement data obtained under the Protocol.
  • Page 108 Absolute path (total folder name from “D:”) of strage folder can’t be over 90 letters. (2) Save Folder Name For each measurement, CQ1 Software prepares a measurement data folder within the data storage folder specified by “Save Setting”, and save images and numerical data. ”Save Folder Name”...
  • Page 109 5-13 <5. Functions of CQ1 Software> Designated in “Save Setting” DataFolder Folder for each measurement data MeasurementData (Folder name is set at “Save Folder Name” Image Folder to store acquired OME-TIFF image Calibration Folder to store calibration data Projection Folder to store projection result (if Z > 1)
  • Page 110 5-14 <5. Functions of CQ1 Software> (4) Protocol List of Protocols saved in Workstation is shown. By selecting a Protocol, its details are shown. Click “x” button on the upper right to close the Protocol detail window. Select protocol Show detail of protocol...
  • Page 111 5-15 <5. Functions of CQ1 Software> (6) Save As Button File save dialog appears by clicking this button to save measurement conditions specified in the control panel. XML file name is shown in the “Name” column of Protocol list. Fill in the outline of protocol.Contents can be confirm in 5.6.7...
  • Page 112 CQ1. (1) Sample Loader Click Open button to open the door on CQ1 Main Unit when the XY-stage is located at the door. Click Close button to close the door when XY-stage moves to the measuring position to get ready for imaging.
  • Page 113 5-17 <5. Functions of CQ1 Software> Selection of sample vessel type (Microplate) Selection of sample vessel type (35 mm dish) Selection of sample vessel type (60 mm dish) IM 80J01A01-01E...
  • Page 114 5-18 <5. Functions of CQ1 Software> Selection of sample vessel type (Slide glass) Selection of sample vessel type (Cover glass chamber) IM 80J01A01-01E...
  • Page 115 5-19 <5. Functions of CQ1 Software> By using “Edit” button at the bottom of “Sample Vessel Type”, it is possible to modify sample shape and create customized sample type. (Example: 35 mm dish) ③ ④ ⑤ ① ② ⑦ ⑧...
  • Page 116 5-20 <5. Functions of CQ1 Software> ① Delete Button Delete the sample vessel type selected in “Sample Vessel Type” menu. Default sample vessel types are key-marked and cannot be removed by Delete Button. ② Edit Button Start editting parameters of selected sample vessel type in “Sample Vessel Type”...
  • Page 117 5-21 <5. Functions of CQ1 Software> ⑦ Save Button Save modified parameters and finish editing. ⑧ Cancel Button Cancel modified parameter setting and finish editing. ⑨ Set Button Overwrite newly set parameters on selected sample vessel type and finish editing. You cannot click this button when a key-marked type is selected.
  • Page 118 5-22 <5. Functions of CQ1 Software> 5.4.3 Imaging Window Imaging window is to specify sample imaging conditions (1) Channels ① ② ③ ④ ⑤ ⑦ ⑧ ⑥ ① Imaging channel list Show the list of imaging channels specified by; “Option” menu →...
  • Page 119 5-23 <5. Functions of CQ1 Software> ② Excitation Power Specify light source power (laser or lamp) in the range of 0.0%~ ※ 100.0% . It is able to specify any way shown following. (The same goes for ③, ④) Direct input...
  • Page 120 5-24 <5. Functions of CQ1 Software> ⑥ Flat Field Correction Correct peripheral image darkness caused by shading of the microscope. (Default: checked) ⑦ Chromatic Aberration Correct chromatic aberration caused by difference of wavelength. (Default: checked) ⑧ Laser Enhancement Check to enhance excitation power. If checked, value of excitation power turns red.
  • Page 121 5-25 <5. Functions of CQ1 Software> (2) Wells ① Slide Glass Sample Holder ② ④ ⑥ ⑤ ⑦ ③ ① Selected sample vessel Diagram of sample vessel selected at “Sample window” is shown. Unselected wells are shown in white. Gray wells are unselectable due to interference of objective lens.
  • Page 122 5-26 <5. Functions of CQ1 Software> ⑤ Clear Selection for Rec of all wells are canceled. This botton is displayed when “Same Area” is checked. ⑥ PreRec Start preliminary imaging of wells selected for Rec. You need to select wells to be images by “Map” window beforehand.
  • Page 123 5-27 <5. Functions of CQ1 Software> ④ Slide Ratio Specify the travel distance when moving the imaging Field by imaging Field shift button. Field size is a travel distance unit. For example, by setting 0.10, the stage moves 1/10 of the Field size, and setting 1.00 moves by one Field size.
  • Page 124 ⑥ ⑦ <About CQ1 autofocus> CQ1 can perform 2 types of autofocus, which are laser based and image based. Laser Autofocus detects surface of bottom plate or cover glass by laser and set the surface as Z base position. Please note that surface to detect (Z base positon) is different by the kind of sample vessel.
  • Page 125 5-29 <5. Functions of CQ1 Software> ① Preview If checked, automatically capture images and show in “ImageViewer” whenever you change Z position. ② Laser AF Autofocus unit detects the interface of cover glass of the sample holder when capturing preview or time-lapse images, and save the Z-zero-position in the system.
  • Page 126 5-30 <5. Functions of CQ1 Software> ⑤ Objective lens information Information of selected objective lens such as model name, magnification and NA and working distance is shown. ⑥ Z Stack Parameter Top is the upper limit of Z Stack, and Bottom is the lower limit of Z Stack.
  • Page 127 5-31 <5. Functions of CQ1 Software> (5) Objective Lens Select objective lens here. Selected lens is highlighted. (6) Time-lapse Setting Switch the time-lapse acquisition mode (normal mode/ fast mode (option)). If you didn’t buy this option, this menu isn’t shown and the time-lapse acquisition mode is always normal mode.
  • Page 128 5-32 <5. Functions of CQ1 Software> (7) Time-lapse Condition Set time-lapse imaging setting in Normal mode ① ② ③ ④ ① Interval Set the interval of time-lapse measurement in seconds. The specified time and acquisition time are shown on the right.
  • Page 129 5-33 <5. Functions of CQ1 Software> ④ Variable Time-lapse An interval change event at a specific time point can be preset. Time Point: Time point to change interval Interval (sec): New interval Past: Time for interval change <In case of constant interval time-lapse>...
  • Page 130 5-34 <5. Functions of CQ1 Software> (8) Fast Time-lapse Condition Set time-lapse imaging setting in Fast mode (option). If you didn’t buy this option, this menu isn’t shown. ① ② ③ ① Total Period Set the term of time-lapse measurement by seconds. The calculated number of acquisition times is shown on the right.
  • Page 131 5-35 <5. Functions of CQ1 Software> ③ Renewal Button Display total image number and total file volume. By clicking this button, total file volume and total image number are renewed. Total image number (Total file volume) If HDD space is not enough, display warning sign.
  • Page 132 5-36 <5. Functions of CQ1 Software> 5.4.4 Application Window Application window is for setting image analysis conditions. (1) Execute Analysis When checked, runs measurement and analysis at the same time, and runs measurement only when unchecked. IM 80J01A01-01E...
  • Page 133 5-37 <5. Functions of CQ1 Software> (2) Load Load Analysis Protocol ◆Load Analysis Protocol (User Window) ① ⑧ ⑤ ⑦ ② ③ ④ ⑥ ◆Load Analysis Protocol (Application Window) ⑨ IM 80J01A01-01E...
  • Page 134 5-38 <5. Functions of CQ1 Software> ◆Load Analysis Protocol (TemplateWindow) ⑩ ① List of Analysis Protocol (User Window) Show the list of protocols saved by user. Name Description Date Date of saving the analysis protocol Name Name of analysis protocol...
  • Page 135 5-39 <5. Functions of CQ1 Software> ⑥ Cancel Close the window ⑦ Other File Load Analysis Protocol from arbitrary protocol. ⑧ Delete Delete Analysis Protocol selected in ①. Protocol selected in ⑨ or ⑩ can’t be deleted IM 80J01A01-01E...
  • Page 136 Protocol for counting objects of multiple categories in individual object image Neurite outgrowth Protocol for analyzing neurite outgrowth ⑩ Analysis Protocol List (Template Window) Show basic Analysis Protocols preloaded in CQ1 Software Name Description Nucleus Protocol for analyze nucleus (one object) Dots in Nucleus...
  • Page 137 5-41 <5. Functions of CQ1 Software> (3) Save Save the Analysis Protocol. ① ② ③ ④ ① Name Define the name of Protocol which is also used as file name. ② Description Input description of the Protocol. ③ Save Save the Protocol.
  • Page 138 5-42 <5. Functions of CQ1 Software> (4) Z Analysis Setting Set the analysis method for multi-Z images. Either one in following table must be selected. Slice 3D image generated from Multi-Z images is analyzed MIP image generated from Multi-Z images is analyzed...
  • Page 139 5-43 <5. Functions of CQ1 Software> ⑥ [>>] Apply selection range of Z slices. ⑦ Unselected Show unselected Z slices for analysis target. Total number of unselected Z slices is shown at the bottom right. ⑧ Selected Show selected Z slices for analysis target. Total number of selected Z slices is shown at the bottom right.
  • Page 140 5-44 <5. Functions of CQ1 Software> ④ Sampling Select time points for analysis target by interval designated by “Skip” or total number of time points designated by “Total”. ⑤ Skip Input interval of time points selection. ⑥ Total Input total number of time points to select.
  • Page 141 5-45 <5. Functions of CQ1 Software> (7) Edit Object Detect Setting Edit object detect settings. Up to 10 objects can be added. ① ⑤ ⑥ ② ③ ④ ⑦ ⑧ ① Object list to detect Show the list of object detect setting...
  • Page 142 5-46 <5. Functions of CQ1 Software> ⑧ Cancel Cancel the modification and close window. (8) Link Setting Show the current Link Setting. The node one-step above the object is called “Root node”, and the one below is called “Sub node”.
  • Page 143 5-47 <5. Functions of CQ1 Software> (9) Edit Link Setting Edit Link Setting. Please note the unlinkable conditions shown below. ・ Sub node cannot be added to an “one-to-many” link. ・ Object Detect cannot be linked to “one-to-one” more than once.
  • Page 144 5-48 <5. Functions of CQ1 Software> ④ Add Add a Sub Node to the selected node. Append Select the Object Detect to be linked. The list of Object Detect Setting is shown. Link Condition Select link condition. Please refer to ◆Conditions of Sub Nodes in (7) Link Setting (page 5-46).
  • Page 145 5-49 <5. Functions of CQ1 Software> ⑤ Edit Edit selected node setting. Append Select the reference Object Detect Setting from the list to be shown. Close window after confirming changes. iii. Cancel Cancel changes and close window. Append Select a reference Object Detect Setting from the list to be shown.
  • Page 146 5-50 <5. Functions of CQ1 Software> ⑥ Remove Remove selected nodes except for Root Node. Root Node cannot be removed. Sub nodes of removed node are also removed altogether. ⑦ OK Close window after confirming link setting. ⑧ Cancel Cancel changes and close window.
  • Page 147 5-51 <5. Functions of CQ1 Software> 5.4.5 Analysis Window Set each method and parameter of Object Detect. (1) Wells This function works after test imaging by “PreRec” at “Imaging” window. ① Black: Not-imaged (Unselectable) Gray: Imaged (Unselected) Red frame: Selected for Preview...
  • Page 148 5-52 <5. Functions of CQ1 Software> (2) Object Detect Algorism Set a series of image processing methods (Object Detect Algorism) and parameters to detect objects, such as nuclei or cytoplasm. Image processing methods will run in order from the top line.
  • Page 149 5-53 <5. Functions of CQ1 Software> ⑥ LabelTransform Method: SizeFilter Filter each labeled region based on its size (area for 2D analysis, and volume for 3D analysis). ⑦ Edit “Advanced Editor” window opens. For detail, refer to 5.13 Advanced Editor.
  • Page 150 5-54 <5. Functions of CQ1 Software> 5.4.6 Environment Window Environment window is to set the operation environment of CQ1 Main Unit. <Stage Heater mounted model> <Stage Heater unmounted model> (1) Temperature Control Activate/ inactivate of stage heater and its temperature.
  • Page 151 5-55 <5. Functions of CQ1 Software> (3) XY Stage Set moving speed of XY stage. [Edit] button is to select XY stage speed. ② ③ ① ① Speed Select XY stage speed. Default setting is the fastest. If samples are easy to ablate from sample vessel, slow setting is recommended.
  • Page 152: Control Panel (Hdd Mode)

    5-56 <5. Functions of CQ1 Software> 5.5 Control Panel (HDD Mode) In HDD mode, click left-side tabs to set analysis conditions and to output data such as screenshot, movie and so on. If measurement data isn’t selected, only the “Protocol” tab is shown on control panel.
  • Page 153 5-57 <5. Functions of CQ1 Software> 5.5.1 Protocol Window In HDD mode, measurement data list which is saved in the folder selected by “Measurement List” is shown at Protocol window. In detailed view, more information is shown than brief view.
  • Page 154 5-58 <5. Functions of CQ1 Software> (1) Measurement Data Folder Full-path-name of the storage folder of measurement data in the list is shown. Click [...] button at the right end to show folder selection dialog where measurement data storage folder can be changed.
  • Page 155 5-59 <5. Functions of CQ1 Software> (5) Existence of Feature Data If quantified data is included in measurement data, 「 」 mark is attached. Click 「 」 mark to show pull down list of feature data. To close this list, click anywhere outside of the list.
  • Page 156 5-60 <5. Functions of CQ1 Software> (6) Date Date and time of the measurement are shown. (7) User Text Show the text in “Save Folder Name” at “Protocol” window of CQ mode. (8) Camera Icon Show that report data such as snapshot exists. It is able to confirm...
  • Page 157 5-61 <5. Functions of CQ1 Software> Show selected re-analyzed data. (15) Description Show the text in “Description” at “Protocol” window of CQ mode. (16) (21) Export Export checked measurement data to other folder or drive. Click this button after selecting measurement data to show folder selection dialog.
  • Page 158 5-62 <5. Functions of CQ1 Software> (18) (19) Read Viewer ※ data in the “Viewer”. Click to show lastly selected Viewer display changes depending on the existence of quantified data as below. ※ Circle mark is shown by lastly selected data.
  • Page 159 5-63 <5. Functions of CQ1 Software> ① ③ ② ④ ⑤ ⑥ ⑦ ⑧ Progress dialog Dialog to notice completion ① Output Option Select the data to export. It is unselectable if there are no data corresponding to original data.
  • Page 160 5-64 <5. Functions of CQ1 Software> ② Tile Transform images acquired by Area imaging to single tiled image and output. For using this function, it is necessary that images are acquired by same condition (“Same Area” in “Imaging” window is checked).
  • Page 161 5-65 <5. Functions of CQ1 Software> ⑥ OK Start data export by set parameter. Progress dialog is displayed after export is started. Dialog to notice completion is displayed after export is completed. Click “OK” and folder that measurement data is exported is opened.
  • Page 162 5-66 <5. Functions of CQ1 Software> 5.5.2 Application Window Application window is to set image analysis conditions of existing measurement data. Please refer to 5.4.4 Application Window details. (1) Analysis Folder Suffix Set suffix of analysis folder name Note Over 30 letters can’t be input for “Analysis Folder Suffix”.
  • Page 163 5-67 <5. Functions of CQ1 Software> (3) Save Save Analysis Protocol (4) Z Analysis Setting Select Z slice images to analyze (5) Time-lapse Setting Select images of time point to analyze (6) Object Detect Setting Show existing Object Detect Setting list...
  • Page 164 5-68 <5. Functions of CQ1 Software> 5.5.3 Analysis Window Set methods and parameters for Object Detect (1) Wells ① Black: Not-imaged (Unselectable) Gray: Imaged (Unselected) Red frame: Selected for Preview Pink: Selected for Analysis ② ③ ④ ⑤ ⑥ ① Selected Sample Vessel Diagram of sample vessel selected at “Sample window”...
  • Page 165 5-69 <5. Functions of CQ1 Software> 5.5.4 Output Window Output images and charts and others displayed in CQ1 software as images in designated folder (Report folder). (1) Image Export ② ⑦ ⑧ ① ⑥ ③ ④ ⑤ ① Output Folder Click to open Report folder.
  • Page 166 5-70 <5. Functions of CQ1 Software> ② Snapshot/ Movie Output snapshot or movie (Only time-lapse data) of displayed content of CQ1 Software. Content and file name to be output are as following. Capture Output Content File Name Image Image shown in Snapshot: “ImageViewer”...
  • Page 167 5-71 <5. Functions of CQ1 Software> ④ Movie Making Conditions Timepoint Designate time point to save movie Begin Time point of movie beginning Time point of movie ending Set “Begin” and “End” to data existing range Express Check to reduce images to convert to movie.
  • Page 168 5-72 <5. Functions of CQ1 Software> ⑥ Convert Click this button to open “Convert Setting” window. Click “OK” to convert images. Merge Option Select method for channel marging Output with color marging. (Output format is PNG or JPG. Merge Color Designate either by “Extension...
  • Page 169 5-87). For detail, please refer to next page Note The purpose of this function is exporting CQ1 data to ImageJ, which is other software. If you don’t use ImageJ whose version is different from that of installed in CQ1 Workstation (1.47v), this function is not guaranteed.
  • Page 170 5-74 <5. Functions of CQ1 Software> Procedure of 3D Viewing ①In “Image Export”, select “Send to” → “ImageJ 3D Viewer” ②Set the configuration of 3D Viewer. After setting, click “OK” ① ② ①Z slice Designate the Z range for 3D projection ②Scale Factor...
  • Page 171 5-75 <5. Functions of CQ1 Software> ④3D Viewer is displayed. Zoom by wheel of mouse. Rotate by left button drag of mouse. ⑤Show the procedures to save snapshot of 3D Viewer. From menu of 3D Viewer, select “View” → “Take snapshot”.
  • Page 172 5-76 <5. Functions of CQ1 Software> ⑦Image of snapshot is displayed. From menu of ImageJ, select “File” → “Save as” and save snapshot in arbitrary format (TIFF, PNG and so on). ⑧Show the procedures to save 3D rotation movie. From menu of 3D Viewer, select “View”...
  • Page 173 5-77 <5. Functions of CQ1 Software> ⑨3D rotation movie is displayed. From menu of ImageJ, select “File” → “Save as” and save 3D rotation movie in arbitrary format (TIFF, AVI and so on). IM 80J01A01-01E...
  • Page 174 5-78 <5. Functions of CQ1 Software> (2) Analysis Data Export ① ② ③ ④ ⑤ ⑥ ⑦ button in “Image Export” to open Report folder. Report folder Click is generated in following path. Folder designated in “Protocol” DataFolder tab→”Save Setting”...
  • Page 175 5-79 <5. Functions of CQ1 Software> ④ ICE Option Check to save mask file in ICE format. ⑤ CSV Output Output data in CSV format Sub folder name and file name in CSU folder is as following Output Output Item...
  • Page 176: Viewer

    5-80 <5. Functions of CQ1 Software> 5.6 Viewer In “Viewer”, captured images, image-detected regions, list of measurement and statistic of feature data, and scattergram of measurement data are shown. 5.6.1 Operation of Viewer Click tab to switch display of each window.
  • Page 177 5-81 <5. Functions of CQ1 Software> Drag tab to move the window. IM 80J01A01-01E...
  • Page 178 5-82 <5. Functions of CQ1 Software> Drag tab to square mark as following to add the tab to the window. IM 80J01A01-01E...
  • Page 179 5-83 <5. Functions of CQ1 Software> Drag tab to center arrow mark as following to allocate as new window by the window. IM 80J01A01-01E...
  • Page 180 5-84 <5. Functions of CQ1 Software> Drag tab to peripheral arrow mark as following to allocate as new window at end of “Viewer”. IM 80J01A01-01E...
  • Page 181 5-85 <5. Functions of CQ1 Software> Click “x” mark in upper right of each window to close selected window. Windows can be set to default position by “Viewer Layout” button. For detail, refer to 5.8 Viewer Layout. IM 80J01A01-01E...
  • Page 182 This operation is same in 5.6.3 MAP Window. <Explanation of term: “Field” and “Area”> CQ1 can image not only one field but also multiple tiled fields. In this section and next section 5.6.3 MAP Window, single field is described “Field” and group of multiple tiled field is described “Area”.
  • Page 183 5-87 <5. Functions of CQ1 Software> ② ① ③ ④ “ImageViewer” has five windows; (1) Image View, (2) Z Stack, (3) Channel, (4) Area, and (5) Thumbnail. Common functions of 5 windows are shown in ①~④, below. ① Time Set the time point to display.
  • Page 184 5-88 <5. Functions of CQ1 Software> (1) Image View Window. It is possible to display multi-channel images as one image by setting Time, Field and Z. IM 80J01A01-01E...
  • Page 185 5-89 <5. Functions of CQ1 Software> (2) Z Stack Window Display tiled images from bottom to top in Z by setting Time and Field. MIP and Sum check box is not available here. Please refer to (6) View Option of 5.6.9 Tool Function (page 5-120) about image size.
  • Page 186 5-90 <5. Functions of CQ1 Software> (3) Channel Window Separately display images of each channel from a multi-channel image by setting Time,Field and Z. Please refer to (6) View option of 5.6.9 Tool Function (page 5-120) for display modes. IM 80J01A01-01E...
  • Page 187 5-91 <5. Functions of CQ1 Software> (4) Area Window Display image of Area by tile. Change to “Area” from “Field” IM 80J01A01-01E...
  • Page 188 5-92 <5. Functions of CQ1 Software> (5) Thumbnail Window Display thumbnail images of wells selected at WellTable window. . Can change Field and Z at each well IM 80J01A01-01E...
  • Page 189 5-93 <5. Functions of CQ1 Software> 5.6.3 MAP Window ① ② ③ ④ MAP viewer has (1) Test imaging mode, (2) Map mode, and (3) Rec mode. Their common functions are shown in ①~④ below. ① Objective lens selection Selected lens is highlighted.
  • Page 190 5-94 <5. Functions of CQ1 Software> (1) Test Imaging Mode Capture test image of clicked Field at a single channel by one-click. Field to be imaged is shown as red square. IM 80J01A01-01E...
  • Page 191 5-95 <5. Functions of CQ1 Software> (2) Map Mode Capture map image by selecting a region by left-drug of mouse. Selected region is shown in green. ① ② ③ ④ ① Start Start map-imaging. ② MultiWell Start Start map-imaging of multiple wells.
  • Page 192 5-96 <5. Functions of CQ1 Software> (3) Rec Mode Set Area(s) to be imaged. Clicked Area is selected and highlighted in orange. Selected Area can be moved by left-drag. ① ② ③ ④ ⑤ ⑥ ① Start Capture test images of selected Area (highlighted by orage frame) at one channel, and display on the map.
  • Page 193 5-97 <5. Functions of CQ1 Software> 5.6.4 ThumbnailChart Window ThumbnailChart has two data display modes, (1) Scatter mode, and (2) Histogram mode. ThumbnailChart1, ThumbnailChart2 and ThumbnailChart3 have the same function. X Axis Y Axis IM 80J01A01-01E...
  • Page 194 5-98 <5. Functions of CQ1 Software> (1) Scatter Mode Display scattergram of measured data. Measured data of wells selected at “WellTable” window are plotted. ⑪ ① ② ③ ④ ⑤ ⑬ ⑥ ⑦ ⑧ ⑨ ⑩ ⑪ ⑫ ⑬ ⑫...
  • Page 195 5-99 <5. Functions of CQ1 Software> ⑦ Color “Same” is to display all wells on a chart in the same color. “Each” is to color wells in different colors by each well. ⑧ Heat Min Color Select the color for low density area in a chart.
  • Page 196 5-100 <5. Functions of CQ1 Software> ⑭ Well, Field Count ※ When region is designated (by mouse dragging ) in chart, show the number of points included in the region by the list. If chart display is Well Merge (above ①, ), number of each well is shown.
  • Page 197 5-101 <5. Functions of CQ1 Software> (2) Histogram Mode Display histograms of measurement data. Measurement data of yellow wells specified at “WellTable”window are plotted. ① ② ③ ④ ⑩ ⑤ ⑥ ⑦ ⑧ ⑨ ⑩ ⑪ ⑪ ① Well Merge Display Display a measurement result of selected wells by one merged chart.
  • Page 198 5-102 <5. Functions of CQ1 Software> ⑥ Resolution Size Change the width (resolution size) of the histogram. By moving slider bar to the right, width of the bar will be extended (to make the resolution size coarser. ⑦ Heat Min Color Set the color of the bar on a chart.
  • Page 199 5-103 <5. Functions of CQ1 Software> ⑪ Well, Field Count When region is designated (by mouse dragging) in chart, show the number of points included in the region by the list. If chart display is Well Merge (above ①, ), number of each well is shown. If chart display is Each Well (above ②...
  • Page 200 5-104 <5. Functions of CQ1 Software> (3) Jump Function The detected object in corresponding image will be shown by clicking a spot plotted in scattergram. On the other hand, a corresponding spot in scattergram will be cross-marked by clicking an object.
  • Page 201 5-105 <5. Functions of CQ1 Software> The detected object in corresponding image will be shown by clicking a bin in histogram. On the other hand, a corresponding bin in histogram will be marked by a vertical line by clicking an object.
  • Page 202 5-106 <5. Functions of CQ1 Software> 5.6.5 WellTable Window In “WellTable” window, it is able to select wells to be shown at ThumbnailChart 1, ThumbnailChart 2 and ThumbnailChart 3 (2), and to select the statistic of feature data of each well (3).
  • Page 203 5-107 <5. Functions of CQ1 Software> (4) Measurement Data Selection By selecting measurement data of each well, the data will be shown at WellTable. The red color becomes deeper proportionally to the relative values. Selectable measurement data are cell number per well and average and standard deviation of data described in 5.6.8...
  • Page 204 5-108 <5. Functions of CQ1 Software> 5.6.6 FeatureTable Window In “FeatureTable” window, it is able to confirm measurement value of detected object such as cell, granule and so on. Please refer to 5.6.8 Measurement Data about shown items. To confirm measurement value, click object in “ImageViewer” or data in either ThumbnailChart.
  • Page 205 5-109 <5. Functions of CQ1 Software> Note Either case that there are no feature data or that cell or granule have never selected, nothing is shown in FeatureTable. In case that range of either axis is designated, the data which is not shown in the chart is not shown at FeatureTable.
  • Page 206 <5. Functions of CQ1 Software> 5.6.7 Information Window “Information” window is, to confirm information of measurement data. This function is only for “HDD mode”. In “CQ1 mode”, display nothing. (1) Comment Show Description of measurement data. (2) Protocol Show Protocol of measurement data.
  • Page 207 5-111 <5. Functions of CQ1 Software> 5.6.8 Measurement Data CQ1 Software outputs following measurement value. (1) 2-Dimentional Measurement Item Description Area Area [µm X-Coordinate X coordinate of centroid [µm] (In reference to upper left of image) Y-Coordinate Y coordinate of centroid [µm]...
  • Page 208 5-112 <5. Functions of CQ1 Software> (2) 3-Dimentional Measurement Item Description Volume Volume [µm X-Coodinate X coordinate of centroid [µm] (In reference to upper left of Z=1-image) Y-Coodinate Y coordinate of centroid [µm] (In reference to upper left of Z=1-image) Z-Coodinate Z coordinate of centroid [µm]...
  • Page 209 5-113 <5. Functions of CQ1 Software> (3) Measurement Value with Link Setting In case that link is set in “Application” window, object name is shown in front of the name of measurement value. Also, in case that one-to-many subnode is set in the link, linked number and average of each feature data is output.
  • Page 210 5-114 <5. Functions of CQ1 Software> 5.6.9 Tool Function Tool Function is to change the display style of image-detected regions in “ImageViewer”, or contrast of images. - Show detected area. - Detected area is shown in “Image View Tab” and ”Thumbnail Tab”.
  • Page 211 5-115 <5. Functions of CQ1 Software> (1) Region Set display options for image-detected region. This setting is applied to only “Image View” window and “Thumbnail” window of “Viewer”. ③ ② ⑤ ① ④ ⑥ ⑦ ① Display detected region Eye-mark shuts or opens by each click.
  • Page 212 5-116 <5. Functions of CQ1 Software> ⑥ Color Select color of detected regions. Invalid if “Multi” is selected. ⑦ Show Object ID Check to show ID of detected regions. IM 80J01A01-01E...
  • Page 213 5-117 <5. Functions of CQ1 Software> (2) Contrast Enhancement Display intensity histograms of images of each channel, and Max. /Min, intensity of displayed images. ⑤ ④ ③ ① ⑥ ② ① Ch Channel number ② Merge Setting Button Eye-mark shuts or opens by each click of this button.
  • Page 214 5-118 <5. Functions of CQ1 Software> ⑤ Automatic Contrast Adjustment By checking [Auto], contrast is automatically adjusted according to the intensity of images. ⑥ Pseudo-color Setting Button Set the pseudo color of displayed image in the current channel. (3) Image Information Show detail information of the image displayed in “ImageViewer”.
  • Page 215 5-119 <5. Functions of CQ1 Software> (5) Overlay Tools Overlay information such as text or size on the displayed images in “ImageViewer”. ① ② ③ ④ ① Scale Bar Add “scale bar” on images. By dragging in “ImageViewer”, position and length can be changed.
  • Page 216 5-120 <5. Functions of CQ1 Software> (6) View Option Slider to change size of images displayed in “ImageViewer”, when “Z Stack” window at “ImageViewer” is open. Items to change display mode in “ImageViewer” are shown when “Channel window” at “ImageViewer” is open.
  • Page 217 5-121 <5. Functions of CQ1 Software> 5.6.10 Progress Bar During measurement, progress information is displayed in upper right of viewer. ① ② ③ ④ ⑤ ① Status Executing process is shown. ② Progress Progress of measurement is shown ③ Elapsed Time Elapsed time of measurement is shown.
  • Page 218: Status Panel

    Status Mode Panel under CQ Mode. Preview: Preview imaging is ongoing Analysis: Analysis is ongoing Connecting: Connection with CQ1 Main Unit is ongoing (6) Progress Status Progress status of measurement is shown by well number (completed wells/total wells) and by the progress bar.
  • Page 219: Viewer Layout

    Change viewer layout for image capturing (2) ImageViewer & Chart Change viewer layout suitable for the analysis of each single cell by using charts (3) Chart Change viewer layout for chart analysis. (4) Information Change viewer layout for viewing information of the CQ1 IM 80J01A01-01E...
  • Page 220: Channel Setting

    5-124 <5. Functions of CQ1 Software> 5.9 Channel Setting (10) (1) Method Select imaging method Note <In case of Transmission Illumination (Phase Contrast) is mounted> If “PhaseContrast” is selected, phase contrast lens must be selected. “BrightField” is unselectable. <In case of Transmission Illumination (Bright Field/ Phase Contast) is mounted>...
  • Page 221 5-125 <5. Functions of CQ1 Software> (7) Remove Remove selected channels. This button is invalid if only one channel is selected. Note If channel which is used in analysis setting, the other channel is applied to the setting automatically. (8) Default Restore channel setting to the default.
  • Page 222: Trimming Parameter

    5-126 <5. Functions of CQ1 Software> 5.10 Trimming Parameter (1) Trimmed image from center Check to trim acquired images by following paremeter. Trimmed area isn’t displayed. In case of tiling images with stitching (refer to page 5-64), check the box.
  • Page 223: User Setting

    5-127 <5. Functions of CQ1 Software> 5.11 User Setting (1) Folder structure of saving data Set folder structure for saving image as following. None: Save all images in 1 folder By Field: Create folders for each Field to save images by Field.
  • Page 224: Activation Setting

    <5. Functions of CQ1 Software> 5.12 Activation Setting CAUTION Please do not operate Activation Setting window except when necessary such as updating CQ1 Software. CQ1 Software might be inoperatable. For updating CQ1 Software, please contact the dealer. ****-**** ****-****-****-****-****-* 1.xx.yy.z (1) MID MID is shown.
  • Page 225: Advanced Editor

    5-129 <5. Functions of CQ1 Software> 5.13 Advanced Editor In the “Advanced Editor” window, “object detecting algorism” which was defined at “Application” window, can be edited. IM 80J01A01-01E...
  • Page 226 5-130 <5. Functions of CQ1 Software> (1) Edit object detecting algorism Object detecting algorism which was defined at “Application” window, can be edited. ① ② ④ ③ ⑤ ⑦ ⑥ ① Selection of Object Select the object detecting algorism. ② Display of Image Click this button to show the image of reference channel used as input image for object detection in “Analysis Viewer”...
  • Page 227 5-131 <5. Functions of CQ1 Software> ③ Addition of Image Processing Method Click ”+” button to show the list of image processing methods which are usable within the processing group. The selected method will be added at the end of the group.
  • Page 228 5-132 <5. Functions of CQ1 Software> Group Method Name Description Labeling DivideEachRegion Attach the same label on adjacent axis EndPointLabeling Attach label on endpoint of center line JuncPointLabeling Attach label on junction point of center line LineLabeling Attach label on center line...
  • Page 229 Click each method name to perform image processing until clicked method and to display the result at “Analysis Viewer”. In “CQ1 mode”, image processing is performable after test imaging (by clicking “PreRec” of “Imaging” window). In “HDD mode”, performable consistently.
  • Page 230 5-134 <5. Functions of CQ1 Software> (2) Analysis Viewer “Analysis Viewer” shows acquired image or processed image. ③ ④ ⑤ ② ⑥ ⑦ ① IM 80J01A01-01E...
  • Page 231 5-135 <5. Functions of CQ1 Software> ① Displaying Image Show following 4 types of image. Call ii, iii and iv processed image. Acquired Image Acquired image of reference channel to use as input image for object detection. This image is displayed by contrast of black →...
  • Page 232 5-136 <5. Functions of CQ1 Software> iii. Binarized Image Processed image after performing methods of “Binarization” or “Binarize Transform” group. This image is displayed by binary image (objects are red and background is black). Finally filtered image is overlapped. Region Image Processed image after performing methods of “Labeling”...
  • Page 233 5-137 <5. Functions of CQ1 Software> ② Time Set time point of image to display. ③ Well Set well to display. ④ Field Set Field to display. Note When above ② – ④ setting is changed, display of viewer returns to acquired image.
  • Page 234 5-138 <5. Functions of CQ1 Software> (3) Analysis Viewer Setting Change the setting of “Analysis Viewer” ① ② ③ ④ ① Single View Mode Display acquired/ processed image by single view. ② Dual View Mode Display acquired/ processed image by dual view.
  • Page 235 5-139 <5. Functions of CQ1 Software> ③ Quad View Mode Display acquired/ processed image by quad view. ④ Before/ After View Mode Display pre-processed image above of window and post-processed image below. In this view, it is convenient to confirm how image processing of the method works.
  • Page 237: Maintenance

    6 Maintenance 6.1 Maintenance of Workstation  System requirement CQ1 system requires system (C:) disk drive whose volume is larger than 200GB.  Keep free space of hard disk drive For measurement, please keep free space of system (C:) disk drive larger than 30GB, and data (D:) disk drive larger than 1GB.
  • Page 239: Trouble Shooting

    ⇒ Wait until the measurement ends. ⇒ It may take time for door opening in case that stage speed is set to low. It might be that the door of CQ1 Main The stage does not run. Unit is open. ⇒ Close it.
  • Page 240 The CQ1 Software does not run. It might be that the CQ1 Software is run before Windows startup process ends. ⇒ Select “CQ1 Software” on Start Menu of Windows.
  • Page 241 ⇒ After while, re-calibrate them. ⇒ In case of failure in re-calibration, ※ please contact the dealer ⇒ Confirm that CQ1 Main Unit is turned on. CQ1 Software freezes. / Change Is the sample loading port open? between “CQ” and “HDD” modes can ⇒...
  • Page 242: Trouble Shooting During Imaging

    ⇒ Set it so the “A1” well locates on the left rear position from the front of CQ1 Main Unit. ⇒ Set it so that 4 corners set on stage precisely. It might be that the slideglass(es) are (is) not set in proper direction.
  • Page 243 <7. Trouble Shooting> Problem Probable Cause / Corrective Action The laser autofocus does not operate Kind of sample vessel might be properly. wrong. ⇒ Confirm that sample vessel corresponds to that of designated in measurement protocol. It might be that sample vessel which is not registered is used.
  • Page 244 If direction of object shift is different, sample vessel might be distorted. If direction of object shift is same, CQ1 might have an abnormality of stage. In this case, please contact ※ the dealer Sample set part of Stage Attachment may be distorted.
  • Page 245 <7. Trouble Shooting> Problem Probable Cause / Corrective Action ⇒ Reset the range of “Search” Z position of bottom of sample vessel function wider by using “▼” button can not be found. beside “Search” button. ⇒ Confirm that sample vessel is set properly.
  • Page 246 For outputting of log file, please refer to page 5-7. 7.2.1 Cleaning Procedure of the Condensation Reducer Click “Sample” tab → “OPEN” Button of CQ1 Software or do long press (3 seconds) of Door OPEN/CLOSE Button of CQ1 Main Unit to open the door.
  • Page 247 <7. Trouble Shooting> Turn the key switch OFF, then turn the power switch OFF.. Power Switch Key Switch Loosen 2 screws and remove sub cover. IM 80J01A01-01E...
  • Page 248 During temperature controlling, water drops are formed on the downside of the bath cover. Please be careful not to drop water inside the equipment when removing bath cover. If water drops inside the equipment, wipe it completely before turning CQ1 on. Water drop IM 80J01A01-01E...
  • Page 249 7-11 <7. Trouble Shooting> If there is water in the bath, remove it by syringe and others. Hold the tube and the block of condensation reducer, slide them right and pull off the tube from the bath. Condensation reducer Rotate the block counterclockwise then pull off the block. IM 80J01A01-01E...
  • Page 250 7-12 <7. Trouble Shooting> If there is dust or water on the 2 holes on the edge of the block, wipe them. If there is dust or water in the slit, wipe them. Slit After cleaning, insert the edge of the block into the slit of the bath and rotate it clickwise.
  • Page 251 7-13 <7. Trouble Shooting> Slide the tube and the block left and insert the tube to the bath hole. Hold the tube and the block then slide them left to insert the tube to the hole until the end. Set bath cover and tighten 4 screws. In case that the screws can’t be fastened properly, adjust position of bath cover so that the screws are fastened properly.
  • Page 252 7-14 <7. Trouble Shooting> Set sub cover and tighten 2 screws. IM 80J01A01-01E...
  • Page 253: Trouble Shooting During Analyzing

    7-15 <7. Trouble Shooting> 7.3 Trouble Shooting during Analyzing Problem Probable Cause / Corrective Action “Pre Analysis” function does not run “Pre Analysis” function does not run in “CQ”mode. after the measurement. ⇒ Change the oprerating mode from “CQ” mode to “HDD” mode, and then run “Pre Analysis”.
  • Page 254 7-16 <7. Trouble Shooting> Problem Probable Cause / Corrective Action It might be that “Select measurement Well(s) can not be selected by “Imaging” / “Analysis” / “Well Table” area” mode is ineffective. windows. ⇒ Click button to set the mode effective.
  • Page 255: Other Trouble Shootings

    7-17 <7. Trouble Shooting> Problem Probable Cause / Corrective Action Measurement data cannot be found Confirm that the folder designated to “Measurement List” is proper. by HDD mode. ⇒ Designate the upper folder of measurement data folder, whose name is as <date_****>. ※...
  • Page 257: Specifications

    <8. Specifications> 8 Specifications 8.1 Details of MS codes 8.1.1 CQ1 Main Unit Model Suffix Code Option Description Code Confocal Quantitative Image Cytometer Laser -L11 Wavelength:488 nm -L21 Wavelength:488, 561 nm -L22 Wavelength:405, 488 nm -L23 Wavelength:488, 640 nm -L31 Wavelength:405, 488, 561 nm...
  • Page 258 <8. Specifications> 8.1.2 Objective Lens Model Suffix Code Option Description Code CQ1TBL CQ1 Objective Lens Holder Objective Lens Holder Position Position No Objective Lens Holder Objective Lens -L002N 2x Dry (NA=0.08) PLAPON2X -L004N 4x Dry (NA=0.16) UPLSAPO4X -L010N 10x Dry (NA=0.40) UPLSAPO10X2 -L020N 20x Dry (NA=0.75) UPLSAPO20X...
  • Page 259 <8. Specifications> 8.1.4 Options Model Suffix Code Option Description Code CQ1PRT Language Japanese English Gas Mixer /MX2-D Gas Mixer Stage Attachment /SAT1 All Wells Imaging Type /SAT2 Chambered Type Sample Holder /HDA01 For Triple 35 mm Dishes /HDA02 For Single 60 mm Dish /HDA03 For Slide Glass (ISO 8037/1) /HDA04...
  • Page 260: General Specifications

    <8. Specifications> 8.2 General Specifications Main Unit Type Standard Model Transmission Illumination Option Confocal Microlens enhanced dual Nipkow disk system Scanning Method Scanning speed 4000 rpm Select 1 – 4 lasers from 405 nm,488 nm,561 nm,and 640 nm Excitation laser wavelength Phase contrast Option:LED transmission...
  • Page 261: Measurement Sample Vessels

    If 1536 well microplate is measured by 2x/ 4x objective lens, multiple wells are measured by one FOV. Therefore in this case, measurement is inhibited. (Warning is displayed.) For details of sample vessels usable in CQ1, please refer to Technical Information (TI 80J01A01-01E). IM 80J01A01-01E...
  • Page 262: Applicable Standards

    <8. Specifications> 8.4 Applicable Standards ◆CE Marking ●EMC Directives: This product belongs to Class A which is designed to be used under industrial environment. If used under household environment, risk of radio interference could arise, and the user may have to take appropriate measures.
  • Page 263 <8. Specifications> EN/IEC 55011 Group 1, Class A Industrial, scientific and medical equipment. Radio-frequency disturbance characteristics. Limits and methods of measurement EN/IEC 61000-3-2 Class A Electromagnetic compatibility (EMC) - Part 3-2: Limits - Limits for harmonic current emissions (equipment input current <= 16 A per phase) EN/IEC 61000-3-3 Electromagnetic compatibility (EMC) - Part 3-3: Limits - Limitation of voltage changes, voltage fluctuations...
  • Page 264 <8. Specifications> ◆CE Marking ●Machinery Directive: ISO12100 Safety of machinery -- General principles for design -- Risk assessment and risk reduction EN/IEC 13849-1 Safety of machinery -- Safety-related parts of control systems -- Part 1: General principles for design EN/IEC 61010-1 Safety requirements for electrical equipment for measurement, control, and laboratory use - Part 1: General requirements...
  • Page 265 <8. Specifications> ● 488 nm laser for excitation - AEL laser safty class: - Maximum output power: 60 mW - Wavelength: 488 nm - Pulse duration & repeating frequency: Continuous mode - Angular subtense: 0.1 rad ● 561 nm laser for excitation - AEL laser safty class: - Maximum output power: 50 mW...
  • Page 267: Warranty Rule

    ●Failures caused by water leakage due to following processing. ■Over filling water into Stage Attachment (Chambered type). Any other damage not attributable to Yokogawa is outside the scope of this warranty. Should you require any repair, please consult Yokogawa.
  • Page 268 <9. Warranty Rule> Manufacturer International Sales Team. Life Science Center Measurement Business HQ Yokogawa Electric Corporation 2-3 Hokuyodai, Kanazawa-shi, Ishikawa 920-0177, Japan Phone +81-76-258-7028 Fax +81-76-258-7029 CSU_livecell_imaging@cs.jp.yokogawa.com E-mail: Web site http://www.yokogawa.com/scanner Please contact the dealer inquiries about this product. IM 80J01A01-01E...

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