User Interface Guide Beginner Mode¶

You will find here the PlanktoScope’s user guide applied to the Lac0scope project for the beginner mode. The 2023 team project have improved this beginner mode in order to facilitate the use of the interface.

As previously mentioned, when you turn on your PlanktoScope, beginner mode is selected. This mode will simplify the display in order to acquire and export images.

From here, you can quickly access any of the available tabs. The buttons are the most used functionnalities of the machine in this mode.

Four others tabs are accessible only through the hamburger menu on the top left of the screen (the three horizontal lines) but you shouldn’t need to access it in beginner mode:

• System Monitoring
• Wifi
• Administration
• Hardware Config

Machine shutdown¶

From this page, you can also shutdown the machine when you are done.

To shutdown the machine, first unlock the shutdown button by clicking on “UNLOCK BUTTON”.

You can then click on “SHUTDOWN”. The machine will ask for a final confirmation and will then shut itself down.

Sample Tab¶

In this page, you can enter all the information regarding the current sample you want to image. This includes the project name, the operator, but also the type of collection device you used.

Depending on the device you choose, the page will change to reflect the needed information.

In the previous image we can see for example that the selected sampling gear is “Single location (with net or bucket)”. This choice requires you to fill in the “Sample location” block (latitude, longitude, date and time) and for this you can either fill them in by hand or fill them in with the “Prefill sample” block which will use the GPS data to fill in the “Sample location” block.

There is also a mechanism of validation of the submitted data. Please be careful to use the format given in example for each input field.

Once all the fields are completed, you can go to the next tab by clicking the -> arrow. This will make sure all the inserted data is valid.

2023 Improvement¶

This year, we only left one choice for the “sampling gear” section in order to have a single choice by default. Moreover, we deleted all the expert section which were not available (non-modifiable grey section in the previous OS image). However, the user can always prefill the location (0 by default), the date and the time if the GPS does not work properly.

Optic Configuration¶

This page allows you to control the optical setup of the acquisition.

In the Optic Characterization block, you can control to turn the light on or not. You also have to choose the optics used in the machine.

The Camera Settings block allows you to change the ISO number and the shutter speed.

The Focus Adjustment block allows you to control the focus stage. With the different buttons, you can choose to move the stage by different values to the right or to the left in order to make the focus.

The Fluidic Manual Manipulation allows you to control the pump. You can change both the flowrate and the volume pumped. If you click on the rotating arrow, it will start the pump for the given volume at the chosen flowrate.

As with all the tabs, once you are satisfied with your focus and your image settings, you can click on “Continue”.

2023 Improvement¶

This year, we added the “shutter speed” which was only on the expert mode. In order to understand the use of this section, we recalled it “exposure time”. Now, the user can directly control the brightness of the image without changing the mode into expert. Moreover, we deleted the “ISO section” and set its value to 200 by default. For the “choose your lens” section, we replaced the lenses focal values with their magnification. Finally, we kept only the 1mm and the 100 um for the translation values in the “focus adjustment” block.

Fluidic Acquisition¶

Finally, this is where the magic happens! You will be able to chose the final parameters of your capture.

First of all, change the Fraction Size of your sample. You can then choose a unique ID for your acquisition, the number of pictures you want to take, the pumped volume (in between images), the delay to stabilize the image and the Flowcell thickness. All those settings will influence the Total imaged volume (the total volume captured during the acquisition) and the Total pumped volume.

2023 Improvement¶

For this page, we only left one choice for the “flowcell thickness” and deleted the “update config” block. This block was deleted because the update of the configuration is already made when the acquisition starts.

Segmentation¶

This page allows you to segment your images, i.e. to cut the different photos taken during the acquisition into objects. To do this you can select the folder containing the images to be segmented and launch the segmentation with the corresponding buttons.

We can also see at the bottom right of the page two buttons that send us to the pages “GALLERY” allowing us to visualize our images/objects and “DOWNLOAD” allowing us to recover our images/objects on a USB key.

2023 Improvement¶

For the segmentation page, the ecotaxa archive is active by default. Moreover, we changed the “download” button at the bottom of the page into “continue”.

Gallery¶

This page allows us, as we said before, to visualize our images or our objects. To display an image we start by choosing if we want to see full images or only objects. Then, we go through the different folders and select the image we want to see in the last block “Pictures”. The i is displayed in the right block and we have two buttons to browse through the images.

We also see at the bottom right two buttons that send us to the pages “DOWNLOAD” allowing us to recover our images/objects on a USB key and “NEW ACQUISITION” which allows us to start again at the first step to start an acquisition.

2023 Improvement¶

For the gallery page, we replaced the “previous” and “next” buttons for the image display, with “previous image” and “next image”. And we replaced also the “new acquisition” button” with “continue” button in order to have the same structure for all the pages.

Download Files¶

This page allows us to download directly the files present on the Raspberry Pi on a USB key.

After you connected your drive, click on “Detect Drive” to make it appear in the list. Once you have selected your USB drive you have different options:

• All” : this choice will allow you to make a complete backup of your images and objects.
• Images” : this choice will allow you to download your complete images, in the same way as on the “Gallery” page you can browse the different folders in order to download only the one you want.
• Objects” : this choice will allow you to download your objects from your images, in the same way as on the “Gallery” page you can browse the different folders in order to download only the one you want.

Once you have made your choice you can check that you are going to download the right file and start the download by clicking on the “BACKUP TO USB” button. Then wait until a completion message is displayed.

You can also delete the files you have selected with the “DELETE FILES” button.

2023 Improvement¶

Finally, for this “download files” page, we only left the “all” and “images” section for the backup.