Webbased application for the Raspberry Pi and the 12 MP HQ camera for taking stills, especially tailored for the use with a (gemmological) microscope.
Connection of the camera to the third tube of a microscope.
The raspberry is intended to be operated in headless mode over wifi. In this way, only the usb-powercord is attached to the pi, which has almost no effect on the mechanical stability of the camera, reducing vibrations (as an ethernet cable will).
These are more or less generic instructions, they are here to have a guide at hand.
- Use a raspberry Pi 3B+ (or better), with a casing
- Install Raspberry PI OS (32bit), preferrably the light version without the desktop ("headless mode") (https://www.raspberrypi.org/documentation/installation/installing-images/)
- Enable SSH (https://www.raspberrypi.org/documentation/remote-access/ssh/), by placing an empty file "ssh" in the boot partition of the SD card
- Enable headless wifi (https://www.raspberrypi.org/documentation/configuration/wireless/headless.md)
- NOTE: Allthough headless configuration is possible, it is my experience that first setup should be done
with keyboard and monitor connected, and then use:
This way errors by yourself, or by the PI, or errors in the OS are much easier to detect.
sudo raspi-config - to enable setting a simple password, use:
sudo passwd pi
Shut the pi down:
sudo shutdown now
And remove the power when it is done. Attach the HQ camera.
After this start the Pi and use it in headless mode. It is sometimes a pain to find the IP of the Pi. Usually I will bind the MAC adress to a fixed IP in the router, and use a symbolic name in the HOSTS file on your PC.
- Enable the camera with raspi-config. Test with raspistill (https://www.raspberrypi.org/documentation/usage/camera/raspicam/raspistill.md).
If no errors are shown, and a file cam.jpg is written, all is well.
raspistill -t 1 -o cam.jpg
Install two necessary applications:
- Git for installing and updating. Of course you could also download a zip, but upgrading later is easier this way. And installing Git is very simple (https://linuxize.com/post/how-to-install-git-on-raspberry-pi/).
- Install Apache and PHP installed (https://www.raspberrypi.org/documentation/remote-access/web-server/apache.md). If you want to use virtual hosts, consult the documentation on raspberry.org.
Clone this repository inside the webroot (normally /var/www/html). In the webroot on the pi enter (note: instead of gemcam you can choose any name you wish, in the remainer of this document, I assume you choose gemcam):
cd /var/www/html
sudo git clone https://github.com/henkrijneveld/Microscope-PiCam.git gemcam
Go to the install directory and execute the install script
cd gemcam
cd install
sudo ./install.sh
Go to your browser:
http://<ip or name of connected pi>/gemcam
Then click the Start Camera button. A picture should be visible (if camera attached).
Errors? open the console log in your browser (F12 key)
User configuration can be done in config/config.overrides.js and config/raspigemcam.overrides.cfg
Go to the installation directory from the webroot, do a git pull, and run install again. Example:
cd /var/www/html/gemcam
sudo git pull
cd install
sudo ./install.sh
The User Interface runs in a webbrowser, open on a different system.
When using a microscope with standard foto software, I ran into the inconvenience that it was necessary during the work to note seperately the material, the magnification and other parameters. Later on I had to change the filename, leading to mistakes and a very cumbursome process. Microscope-PiCam let you specify the filename with alle relevant information. This results in meaningfull filenames like: garnet-1.5x-0.5R-inclusion-20210321-210304.jpg. Files are downloaded to your system, and stored in a mediafolder on the Pi itself. Maybe it seems strange at first, ben when you start copying files it is a very convenient way to not get confused.
The second problem using the camera's is focussing. A (gemmological) stereo microscope has objectives somewhat tilted from the horizontal plane to achieve the 3D effect. In Microscope-PiCam, you see a preview (in reduced resolution: 1024px. Full picture resolution will be 4056px). However, with a 400% magnification it is possible to get good focussing.
The whitebalance is an other issue. Through the microscope you can seldom use the balancing out of the box. Microscope-PiCam let you manually select the gains in red and blue (green stays constant as part of the design of the HQ camera). By carefully obsering the image, comparing it to the image in the microscope it can be fine tuned to achieve the right colors. Note that white balancing is processed on the camera, so 10 or 12 bits are used (raw processing). An additional grey card (with white, 18% grey, and black) can be helpfull.
The other controls can be set to get the most detail and dynamic range. Look at the live-histogram to avoid clipping. Sometimes the camera will need less light then the eye, so also play with the brightness controls on your microscope.
Note that the primary driver for the quality of the picture is the reduction lens between microscope and camera. I use a rather cheap model. Before I finished writing Microscope-PiCam, it was less noticable...
In use with a synthetic hydrothermal emerald.
The software was developed with phpstorm, and the pi was connected as a remote server.
The UI can be developed (for a part) with no Pi connected. Go to the docker subdirectory and start:
cd /var/www/html/gemcam/docker
# start docker
./start.sh
# refresh docker after changes to the docker files itself
./refresh.sh
# enter the docker image
./gotowebserver.sh
# stop and remove all containers on your PC
./stopandremove.sh
You can use the testsystem on localhost. When the software detects that localhost is used, it will show two images as testimage. Note, that the camerasettings can be adapted, but will have no effect (the settings are processed in the camera modul itself, so when it is not attached, nothing will happen to the picture).
None, anybody on the same (w)lan can access the camera.
The application is meant to be connected to a pc in the direct vicinity of the microscope/camera. All security must be implemented by using a dedicated wifi wlan. For technical reasons, the apache user (www-data) runs with full sudo rights, no password necessary. Making this secure would require a lot of extra effort with no pay-off in this use case. Highly recommended to make this application not available on a broader network.
Air bubbles in resin filled cavity of a bumlbee jasper (horizontal field of view 3mm).
- It is tested only on my own systems: 2 Raspberry 3B+ with a camera connected. I expect some difficulties for first time users.
- This is my first Vue application. There are still some quirks in the event handling. It runs with vue.js in development mode.
- Error messages on the UI itself are almost absent. When an error occurs, it is best to go to the development tools in the browser (F12 key), and inspect the log in the console.
- Shutter speed, analog gain and digital gain are not implemented yet. They work in conjunction, and the latter two are not implemented in the camera driver (raspigemcam), yet.
- On firefox, after longer use I noticed sometimes the network performance of the application degrades.
The mediabrowser is the "Tiny File Manager" script (https://tinyfilemanager.github.io), renamed to index.php in php/filemanager. The config.php used with this filemanager is adapted to automatically set the media directory to the media subdirectory under the site root.
The gemcamdriver is from https://github.com/henkrijneveld/userland, subdir raspigemcam-bin. It is a non-backwards compatible adapted copy from raspimjpeg. For more information, see the readme accompanying the aforementioned repository.
The vue script is from vuejs.org
The general idea of Microscope-PiCam is based on RPi_Cam_Web_Interface (https://github.com/silvanmelchior/RPi_Cam_Web_Interface). This is a very generic application with a lot of functionality of no use for still fotography. I considered the userinterface suboptimal for my goals. Unfortunately, the UI was based on plain javascript and ajax. Vue seems a better choice nowadays. The wiki of this project can be of use: https://elinux.org/RPi-Cam-Web-Interface