diff --git a/docs/usage/pro/frame/guides/day-2/calibrate-pixel-size/README.md b/docs/usage/pro/frame/guides/day-2/calibrate-pixel-size/README.md index 329831138..f1c80f575 100644 --- a/docs/usage/pro/frame/guides/day-2/calibrate-pixel-size/README.md +++ b/docs/usage/pro/frame/guides/day-2/calibrate-pixel-size/README.md @@ -24,11 +24,11 @@ Sample: Calibration target In the picture below you see a properly focused and positioned structure of a calibration sample in the *live view* app. The actual structure used for the procedure will be the upper right hand corner of the 4x4 square (marked with a red arrow). -`Note` This structure is positioned in the lower left hand corner of the live view image due to the range of movements performed later in the calibration process. +`Note` This structure is positioned in the lower right hand corner of the live view image due to the range of movements performed later in the calibration process. ![20x-Pixel-Calibration-start-arrow](./20x-Pixel-Calibration-start-arrow.png) -After switching to the *FRAME settings* app and the tab *Manual pixel calibration*, please, follow the *Four-point calibration Workflow*. Click on *Backlash compensation X*. This moves the sample in X by the depicted amount in the same direction, as it will be moved in the following calibration step (e.g. 50um). This ensures that any backlash from the X-axis is eliminated prior to the following calibration step. +After switching to the *FRAME settings* app and the tab *Manual pixel calibration*, please, follow the *Four-point calibration Workflow*. Click on *Backlash compensation X*. This moves the sample in X by the depicted amount in the same direction, as it will be moved in the following calibration step (e.g. 50um). This ensures that any backlash from the X-axis is eliminated prior to the following calibration step (see [axis-backlash](../axis-backlash/README.md)) for more information on Axis backlash). The next step is *Mark feature (P1 before X move)*. Click on the structure of your choice (here the corner) and a green cross-hair A1 will appear. Then click *Move stage in X* and the stage will be moved by the depicted amount in X (e.g. 100um). Make sure travel range does not exceed the live view window (structure not visible anymore). Then click *Mark same feature (P2 after X move)*. A second green cross-hair A2 and a line will appear. At the bottom of the image you will also see Pixel information for point A1 and A2 including the delta and the subsampling rate. diff --git a/docs/usage/pro/frame/guides/day-2/calibrate-stage/README.md b/docs/usage/pro/frame/guides/day-2/calibrate-stage/README.md index 17ef01d1f..f740759a4 100644 --- a/docs/usage/pro/frame/guides/day-2/calibrate-stage/README.md +++ b/docs/usage/pro/frame/guides/day-2/calibrate-stage/README.md @@ -15,7 +15,6 @@ Stage calibration is recommended if you notice, that when navigating to specific ## Calibration Workflow -Choose a sample slide for calibr Put the *openUC2 Pinhole Slide* in Slot 1 of the 4x sample holder. For stage calibration the pinhole *0.6/0.3mm* in the center of the slide will be used. It is designwise in the center of the slide, so it does not matter whether the sample is rotated or flipped. The distance from this middle pinhole to the edges of the probe is known and stored as reference value in *Imswitch*. ![openuc2-pinhole-slide](./openuc2-pinhole-slide.jpeg) diff --git a/docs/usage/pro/frame/guides/day-2/controller/Controller-charging.jpeg b/docs/usage/pro/frame/guides/day-2/controller/Controller-charging.jpeg new file mode 100644 index 000000000..87f6228cd Binary files /dev/null and b/docs/usage/pro/frame/guides/day-2/controller/Controller-charging.jpeg differ diff --git a/docs/usage/pro/frame/guides/day-2/controller/ImSwitch-settings-bluetooth-pairing.png b/docs/usage/pro/frame/guides/day-2/controller/ImSwitch-settings-bluetooth-pairing.png new file mode 100644 index 000000000..3d6109405 Binary files /dev/null and b/docs/usage/pro/frame/guides/day-2/controller/ImSwitch-settings-bluetooth-pairing.png differ diff --git a/docs/usage/pro/frame/guides/day-2/controller/ImSwitch-settings-bluetooth-pairing2.png b/docs/usage/pro/frame/guides/day-2/controller/ImSwitch-settings-bluetooth-pairing2.png new file mode 100644 index 000000000..70481ca2e Binary files /dev/null and b/docs/usage/pro/frame/guides/day-2/controller/ImSwitch-settings-bluetooth-pairing2.png differ diff --git a/docs/usage/pro/frame/guides/day-2/controller/README.md b/docs/usage/pro/frame/guides/day-2/controller/README.md index d7cedc867..0cbecfc2f 100644 --- a/docs/usage/pro/frame/guides/day-2/controller/README.md +++ b/docs/usage/pro/frame/guides/day-2/controller/README.md @@ -1,35 +1,42 @@ --- -sidebar_label: Game controller +sidebar_label: Controller sidebar_position: 60 --- # Using the game controller to move the stage -:::note Draft outline -Scaffold. Replace the bullet prompts with your own text and delete this banner when done. -::: +This documentation guides you through specifics on "How to pair your controller with your FRAME?" and "How to use the controller?". -*How-to, for operators.* Pair and use a PS4/Bluetooth controller to jog the stage. +## Gamepad Concept + +For a description of all buttons and joysticks see the picture below. + +![controller-gamepad-description](./controller-gamepad-description.jpeg) ## Pair the controller -- Put the controller in pairing mode; connect via Bluetooth. +First, make sure that the controller is sufficiently charged. To charge it use the USB3 input and the included cable. + +![Controller-charging](./Controller-charging.jpeg) + +Put the controller in pairing mode by first pressing and holding the *Share/Turbo* button and then pressing the *home* button until the light bar starts blinking. + +![Bluetooth controller pairing](./controller-bluetooth-pairing.png) + +In ImSwitch go to *settings* and select *Updates* from the dropdown menu. This brings you to the *ImSwitch UI - SystemUpate* page. + +![ImSwitch-settings-bluetooth-pairing](./ImSwitch-settings-bluetooth-pairing.png) + +Toggle the button *Enable UC2 hardware control* to on. The button *Bluetooth Pairing* becomes now available (blue). Click the button and pairing starts. -![Bluetooth controller pairing](./IMAGES/bluetooth-pairing.png) -*Pairing via ImSwitch → Hardware Settings → System Update → "Bluetooth pairing" -(from FAT #0007 Part 2).* +![ImSwitch-settings-bluetooth-pairing2](./ImSwitch-settings-bluetooth-pairing2.png) -:::note TODO -Reused from Notion `FAT FRAME #0007 Korea - Part 2`. More pairing screenshots -(`grafik 1..25.png`) are in that folder if you want a step sequence. -::: +After succesful pairing the light bar of the *game controller* stops blinking and looks like in the below picture. -## Control mapping +![controller-paired](./controller-paired.jpeg) -- Which sticks/buttons move X/Y/Z, change speed, trigger capture. -- Note the axis-direction convention. +## Use the controller -:::note TODO -Notion source: `FAT FRAME #0007 Korea - part 7`/`Part 8` ("PS4 Controller direction"). -Reference: [coordinates and axes](../../../reference/coordinates-and-axes/README.md). -::: +Use the joystick R3 to move X and Y axis. +Use the joystick R4 to move coarse Z. +Use the L2 and R2 button to move fine Z. diff --git a/docs/usage/pro/frame/guides/day-2/controller/controller-bluetooth-pairing.png b/docs/usage/pro/frame/guides/day-2/controller/controller-bluetooth-pairing.png new file mode 100644 index 000000000..7d3b057bd Binary files /dev/null and b/docs/usage/pro/frame/guides/day-2/controller/controller-bluetooth-pairing.png differ diff --git a/docs/usage/pro/frame/guides/day-2/controller/controller-gamepad-description.jpeg b/docs/usage/pro/frame/guides/day-2/controller/controller-gamepad-description.jpeg new file mode 100644 index 000000000..6951f037d Binary files /dev/null and b/docs/usage/pro/frame/guides/day-2/controller/controller-gamepad-description.jpeg differ diff --git a/docs/usage/pro/frame/guides/day-2/controller/controller-paired.jpeg b/docs/usage/pro/frame/guides/day-2/controller/controller-paired.jpeg new file mode 100644 index 000000000..d8d8147e6 Binary files /dev/null and b/docs/usage/pro/frame/guides/day-2/controller/controller-paired.jpeg differ diff --git a/docs/usage/pro/frame/tutorials/day-1/first-sample/README.md b/docs/usage/pro/frame/tutorials/day-1/first-sample/README.md index ef2cb87dd..f9a3596fa 100644 --- a/docs/usage/pro/frame/tutorials/day-1/first-sample/README.md +++ b/docs/usage/pro/frame/tutorials/day-1/first-sample/README.md @@ -34,7 +34,7 @@ As we can see above, first one shorter edge of the microscope slide is placed ag Now you can let go of the spring-loaded edge: ![slide holder: let go of spring-loaded edge](./slide-holder-insert-let-go.jpg) -Now that we've inserted your first sample on a microscope slide, we can continue to the tutorial section to [position your sample for imaging](#position-and-properly-view-your-first-sample). +Now that we've inserted your first sample on a microscope slide, we can continue to the tutorial section to [Open the ImSwitch Live View App](#open-the-imswitch-live-view-app). ### Inserting a well plate @@ -44,7 +44,7 @@ Take a well plate with a sample and place its A1 corner into the corner with the | ------------------------------ | --------------------------- | | ![well-plate holder: insert into corner with button](./well-plate-holder-insert-button.jpg) | ![well-plate holder: insert into opposite corner](./well-plate-holder-insert-opposite-corner.jpg) | -Now that we've inserted your first sample on a well plate, we can continue to the tutorial section to [position your sample for imaging](#position-and-properly-view-your-first-sample). +Now that we've inserted your first sample on a well plate, we can continue to the tutorial section to [Open the ImSwitch Live View App](#open-the-imswitch-live-view-app). ## Open the ImSwitch Live View App @@ -56,7 +56,7 @@ Once you open the Live View page, it will look something like this: ![Live-view-ImSwitch-1-Streamoff](./Live-view-ImSwitch-1-Streamoff.png) -This preview stream was not yet started, so the indicator in the upper right corner is grey and says "Paused)". To start the stream click on the green *Start* button below the image. +The preview stream was not yet started, so the indicator in the upper right corner is grey and says "Paused". To start the stream click on the green *Start* button below the image. An image will appear and the indicator changes to red saying "LIVE - 8.0 FPS" which indicates that the preview is a live preview with a frame rate of 8 FPS (Please, note, that in the picture below illumination is already turned on and the sample is in focus). ![Live-view-ImSwitch-2-streamon](./Live-view-ImSwitch-2-streamon.png) @@ -76,7 +76,7 @@ Now we'll adjust all necessary parameters to position and properly view your sam ### Turn on illumination First, we'll need to illuminate the sample. -In the right column of the *Live View* App, which has the *Stage Control* and *Autofocus* sections, scroll down to the "Illumination" section. Depending on your customer specific configuration you will see all illumination sources available to you - *LED* is always available. On default all illumination sources are switched off - to switch the *LED* on toggle the button on the right to *On*. Then set the LED Power by either sliding the scale or type in a value between 0 and 1023 to the right of the sliding scale. +In the right column of the *Live View* App, which has the *Stage Control* and *Autofocus* sections, scroll down to the "Illumination" section. Depending on your customer specific configuration you will see all illumination sources available to you - *LED* is always available. On default all illumination sources are switched off - to switch the *LED* on toggle the button on the right to *On*. Then set the LED Power by either sliding the scale bar or type in a value between 0 and 1023 to the right of the sliding scale. ![Live-View-ImSwitch-4-LEDonly](./Live-View-ImSwitch-4-LEDonly.png) @@ -156,13 +156,13 @@ For more information, please refer to the [Preview Image Settings](../../../guid ## Save Streaming Presets -Now that you have done all the work to find the best parameters for an optimum *live view image* with the active camera and objective, we recommend saving all these parameters as a *Stream Preset*. This allows you to (re)load these settings at any point in time, e.g. after switching cameras or objectives which typically need other settings. +Now that you have done all the work to find the best parameters for an optimum *live view image* with the active camera and objective, we recommend saving all these parameters as a *Stream Preset*. This allows you to (re)load these settings at any point in time, e.g. after switching cameras or objectives which typically needs other settings. You can find the *Stream Presets* section in the main column of the *Live View* App underneath the preview window. If you have not yet saved any preset it will look like the picture below. ![Stream-Presets](./Stream-Presets.png) -Press *Save Current* and a pop-up window opens. It will show you all current parameters saved in this particular *Stream Preset*, asks you to enter a *Preset name* and gives you some Checkbox options on what or what not to include in saved parameter set (on default all boxes are ticked). +Press *Save Current* and a pop-up window opens. It will show you all current parameters saved in this particular *Stream Preset*, asks you to enter a *Preset name* and gives you some Checkbox options on what or what not to include in the saved parameter set (on default all boxes are ticked). ![Stream-presets-popup](./Stream-presets-popup.png) @@ -170,7 +170,7 @@ Press *Save* and the *Stream Preset* section will now show that there is 1 saved ![Stream-Presets-saved](./Stream-Presets-saved.png) -`Important`These settings are stored in your browser´s cache. If you switch browsers or computers they will not be available anymore (redo). +`Important`These settings are stored in your browser´s cache. If you switch browsers or computers they will not be available anymore (You will then need to redo the procedure). ## Save and view your first image @@ -178,8 +178,8 @@ To save your first image of your sample, go to the "Capture" panel below the cam ![Capture-Section](./Capture-Section.png) -Enter a brief name for the image in the *Description* textbox, select your preferred file format (default TIFF) and press -- *Snap*: this stores the image on the SD card of the machines RPI. You can access it by either clicking *Go to folder* or switch to the *File Manager* App located in the ImSwitch Navigation bar on the left. Either way you will see something like in the picture below. To see the recorded image go to the folder *Recordings* and the subfolder with the current date and you will find your image. Double click on the image file and you will get a preview within ImSwitch. +Enter a brief name for the image in the *Description* textbox, select your preferred file format (default TIFF) and press either: +- *Snap*: this stores the image on the SD card of the machines RPI. You can access it by either clicking *Go to folder* or switch to the *File Manager* App located in the ImSwitch Navigation sidebar. Either way you will see something like in the picture below. To see the recorded image go to the folder *Recordings* and the subfolder with the current date and you will find your image. Double click on the image file and you will get a preview within ImSwitch. ![File-manager](./File-manager.png) diff --git a/docs/usage/pro/frame/tutorials/day-1/operational-readiness/README.md b/docs/usage/pro/frame/tutorials/day-1/operational-readiness/README.md index 9969bc094..ac9f0eaf2 100644 --- a/docs/usage/pro/frame/tutorials/day-1/operational-readiness/README.md +++ b/docs/usage/pro/frame/tutorials/day-1/operational-readiness/README.md @@ -50,7 +50,7 @@ To see the current calibration you have two options. ![Objective-Pos2-Live-View](./Objective-Pos2-Live-View.png) -*Option 2:* In the App sidebar menu on the right go to the App *FRAME Settings* (how to enable this app see ). Choose the tab *Objective Controller*. The settings for both objectives including Pixel Size are displayed at the top. +*Option 2:* In the App navigation sidebar on the left go to the App *FRAME Settings* (how to enable this app see ). Choose the tab *Objective Controller*. The settings for both objectives including Pixel Size are displayed at the top. ![Im-Switch-App-Sidebar](./Im-Switch-App-Sidebar.png) diff --git a/docs/usage/pro/frame/tutorials/day-2/stitching-scan-on-a-slide/README.md b/docs/usage/pro/frame/tutorials/day-2/stitching-scan-on-a-slide/README.md new file mode 100644 index 000000000..7c1e5c3d9 --- /dev/null +++ b/docs/usage/pro/frame/tutorials/day-2/stitching-scan-on-a-slide/README.md @@ -0,0 +1,207 @@ +--- +sidebar_label: Stitched Scan on a slide +sidebar_position: 20 +--- + +# Run a large-area (stitched) scan on a slide + +A single camera frame only sees a tiny part of your sample. In this tutorial you'll define a region on one slide, let the FRAME image them *tile* by *tile*, and view the *tiles* stitched into one large overview image. One *tile* equals one image captured at a specific position with predefined *image capture settings*. You can use what we call the *Experiment Controller* of the *Wellplate App* to define, save and run your experiment with all those predefined settings. + +## What stitching is + +- The stage moves the sample under the fixed objective in a grid of positions. +- One image or *tile* is captured at each position with the predefined *image capture settings*. Positions are partly overlapping to ensure proper stitching. +- Overlapping *tiles* are stitched together = merged into one single image. + +## Before you start + +- On your Heidstar sample holder insert at least one sample in one of the 4 positions available. +- Select the camera and objective you want to run your experiment with and obtain a properly illuminated and focused image in the *preview* window of the *Live view* App (see [Insert your first sample](../../day-1/first-sample/README.md#insert-your-first-sample)). +- (Recommended) Move roughly to the center of your large-area scan. + +## Step 1 — Go to the *Wellplate* App + +In the navigation sidebar go to the *Wellplate* App. It will look like the pictures below. + +![Wellplate-App-start](./Wellplate-App-start.png) + +![Wellplate-App-start2](./Wellplate-App-start2.png) + +Let us do a quick tour. You will see 2 main columns. + +In the left column +- the default tab is *Plate map*. For running your first large area image scan this is the only tab we need. +- Underneath an outline of your sample holder area is sketched. Choose your *Layout* - in this case *4 slide Heidstar* - from the dropdown menu just below the outline. +`Note` If no layout is selected the outline will just be blank (white). +- You see some further option at the bottom in this column such as *Reset View* or *Single* or *Well* and many more, which we will come to explain later. + +In the right column - the *Experiment Controller* - +- there is a small symbol in the upper right hand corner which allows you to open a popup window with a *camera live view*. When you hover over it, this is what you will see. + + ![Wellplate-App-preview-button](./Wellplate-App-preview-button.png) + + If you open the *camera live view* it will look something like this. You can reposition and resize the *live view* window. + + ![Wellplate-App-preview-window](./Wellplate-App-preview-window.png) + +- Below is a row with a green *Start* button. We will come back to this row at the very end, when everything is ready to start the scan. +- Below that are a number of tabs in a given order, which all contain settings for your scan. We will go step by step through them in a minute. +- At the very bottom indicates a summary of your settings. Since we have not done any settings yet, it will fill up soon. + - *Positions*: indicates how the number of positions selected on which an image will be taken. + - *Channels*: indicates the number of available channels. + - *Z-Planes*: is either one or a number large than one, if you choose to do a Z-Stack. + - *Timepoints*: is either one or a number larger than one, if you have selected to (re)capture at certain time intervals. + - *Est. Duration* and *Est. Size* give a first order approximation of the time your scan will need on this machine and the total storage needed for all files (currently all Zero). "0 images" shows that currently zero images will be taken, here the total number of images in your experiment will be calculated. + +Now, let us start! We recommend to go through the tabs of the *experiment controller* in the given order from left to right. + +## Step 2 — Choose your area or positions + +The first tab in the *experiment controller* (right column) is the *Positions* tab. +Here are some of the main options to add positions: + +### Add single points + +If you want to add single points make sure the button *Single* in the bottom row of the right column is selected. Move to the position of your choice on the sample by switching to the *Live View* app (see [First Sample](../../day-1/first-sample/README.md)). `Good to know` Your settings in the *wellplate* app do not get lost. + +![Wellplate-App-add-current](./Wellplate-App-add-current.png) + +Now switch back to the *wellplate* app and press *Add current stage position*. This will add the current position (X/Y/Z) to the list of points. + +![Wellplate-App-add-current2](./Wellplate-App-add-current2.png) + +You can also use the *live view* popup window in the *wellplate* app to move to your positions of interest, it is not as handy as the *Live view* app. If you roughly know where your structures are located on your slide you can also select *Move* instead of *Single* in the bottom row and just click in the outline of your slide in the *Plate map* on a position. The stage will move your sample to this position. You can check it in the *live view* popup and add this position by switching back to *Single* and press *Add current stage position*. + +You can add as many points to the list as you like. + +To review your selection you can either Zoom in into the slide view and you will see the point(s) selected indicated (in this case red square). If you click on it, the stage will move to this position. + +![Wellplate-App-add-current3](./Wellplate-App-add-current3.png) + +You can also use the up-and-down arrow to the right of the displayed coordinates to move to the position. YOu can delete the entry by pressing the *Recycle Bin* symbol. + +![Wellplate-App-movetopoint](./Wellplate-App-movetopoint.png) + +### Add an area + +If you want to add an area make sure the button *Area* in the bottom row of the left column is selected. It is helpful to add a single point roughly at the center of your area first. This point will be displayed in the *Plate Map* (see [Add Single Points](#add-single-points)). You can delete it later. + +Now zoom in the *Plate Map* and use the cursor to span an area of interest around the single point you have marked before. Click with the cursor in the upper left corner of your area of interest and draw a rectangle of the size of your desired area. The software will automatically display a grid of positions. + +![Wellplate-App-area-select1](./Wellplate-App-area-select1.png) + +![Wellplate-App-area-select2](./Wellplate-App-area-select2.png) + +Once you are done your scan area will appear as one row in the list of points. You can review any position by clicking on it in the *Plate Map*. + +The status row at the bottom of the left column is updated accordingly and shows you the total number of images and other information. + +![Wellplate-App-area-select3](./Wellplate-App-area-select3.png) + +For the purpose of testing here is an example with just a 3x3 array of positions (9 images). + +![Wellplate-App-area-select4](./Wellplate-App-area-select4.png) + +## Step 3 — Add Channels + +The *experiment controller* allows you to add one ore more *channels* to your experiment. A channel equals one of your available illumination sources - LED, laser and others. What sources are available to you depends on your specific hardware configuration. *LED* for brightfield imaging is in most cases available. + +Move to the second tab *channels*. In the below picture 5 *channels* = illumination sources are available for this specific machine. None of them is active, which you can see in the summary in the tab itself (0/5 channels). + +![Wellplate-App-channels1](./Wellplate-App-channels1.png) + +On default all *channels* are *off*. To activate a channel toggle the greyed toggle bar on the right to *on*. It will turn green. You can also see specific illumination settings for this channel in the dropdown menu. + +![Wellplate-App-channels2](./Wellplate-App-channels2.png) + +To adjust the illumination settings you have 2 options: +- (recommended): if you have not already done so adjust all relevant settings in the *Live view* app. Then press the purple button *read and apply current exp(gain/LED settings* and all current settings will be saved for this channel and used in your experiment. +- Adjust the settings manually. + +If you select more than one channel the *experiment controller* will run a sequence of all activated *channels* on all positions with the settings defined. + +## Step 4 — Choose or verify your objective + +If you move on to the next tab *objectives* your active objective will be displayed and usually that is the one you work with. +`Important` If you switch objectives here, please, verify again, that the illumination settings under *channels* match your chosen objective. + +![Wellplate-App-objective](./Wellplate-App-objective.png) + +## Step 5 — Choose focus and Z-Stack parameters + +The next tab *Z/Focus* allows you to choose focus options and how many different Z-planes you want to image at each position of your experiment. These are your options: + +![Wellplate-App-Z-Focus-Single](./Wellplate-App-Z-Focus-Single.png) + +Let us go through them one by one: +- *Single Z* takes images only in one Z-plane at each position defined in the positions list and at the Z-value defined in the position list. +`Important` No autofocus will be performed. It is assumed that your sample is well focussed at the Z-value defined in the position list. + +- *Autofocus* takes images only in one Z-plane at each position defined in the positions list and runs the Autofocus with the parameters defined at EACH position. +You can choose between software and hardware autofocus (if the latter is available in your hardware configuration). `Recommended` For software autofocus choose software method *Z-sweep (Scan)* and Illumination channel *LED*. +`Important` This increases experiment time significantly. + +![Wellplate-App-Z-Focus-Autofocus](./Wellplate-App-Z-Focus-Autofocus.png) + + +- *Z-Stack* takes images in several Z-plane at each position defined in the positions list. Use the settings menu to define the Z-planes. +`Important` No autofocus will be performed. It is assumed that your sample is well focussed at the Z-value defined in the position list. + +- *Z-Stack + Autofocus* takes images in several Z-plane at each position defined in the positions list AND runs the Autofocus with the parameters defined once at the start of each Z-stack. +`Important` This increases experiment time significantly. + +For more advanced settings go to the dropdown menu *Advanced Settings* at the bottom. + +## Step 5 — Define a focal plane + +The next tab *Focus map* allows you to define a focal plane. This is helfpul if you want to perform a larger area scan and your sample is tilted. The algorithm will let you define the best focal plane for your scan area and apply this during the scan. + +pictures and settings tbd + +## Step 6 — Repeat your experiment in certain time intervals + +The next tab *Time* allows you to repeat your experiment in certain time intervals. + +pictures and settings tbd + +## Step 6 — Parameters for stitching your scan + +The next tab *Tile* allows you to define settings on how your scan shall be performed, so that stitching the individual images of your scan gives optimum results. + +First you can define the overlap of the images - 20% is recommended for good stitching results. + +Next you can choose your scan pattern. + +![Wellplate-App-Tiling](./Wellplate-App-Tiling.png) + +In the dropdown menu *Stitching* you can choose between +- *None*: This will only save your individual files and you can perform stitching with the software of your choice. +- *Full Stitch*: will generate a stitched TIFF. +- *Ashlar Stitch*: will generate a stitched TIFF using Ashlar. The dropdown menu shows you teh default Ashlar Stitching parameters, which you can modify. +`Important` This will significantly increase your experiment time. + +![Wellplate-App-Tiling2](./Wellplate-App-Tiling2.png) + +![Wellplate-App-Tiling-Ashlar-Stitch](./Wellplate-App-Tiling-Ashlar-Stitch.png) + +## Step 7 — Output File Parameters + +The last tab *Output* allows you to define the type(s) of output file formats generated and saved. If active (toggle slide bar to the right so that it turns from grey to blue) a file with the described format will be saved. All selected file formats will be generated. + +![Wellplate-App-Output](./Wellplate-App-Output.png) + +At the bottom you will find the *Ashlar Stitching* toggled on or off depending on your choice in the tab *Tile*. + +![Wellplate-App-Output2](./Wellplate-App-Output2.png) + +## Step 8 — Run your scan + +You are all set now and you can start your scan/experiment/run by pressing the green *Start* button in top row of your experiment controller. + +![Wellplate-App-Run-Stitch](./Wellplate-App-Run-Stitch.png) + +## Related + +- [Acquire a Z-stack](../z-stack/README.md) +- [Keep a big scan in focus with a focus map](../focus-map/README.md) +- How-to (after you've learned it): [pixel-size calibration](../../../guides/day-2/calibrate-pixel-size/README.md) diff --git a/docs/usage/pro/frame/tutorials/day-2/stitching-scan-on-a-slide/Wellplate-App-Output.png b/docs/usage/pro/frame/tutorials/day-2/stitching-scan-on-a-slide/Wellplate-App-Output.png new file mode 100644 index 000000000..e7c8964f7 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