In my lab, I have a nice, inexpensive setup for capturing microscope images. About 10 years ago, I bought a dedicated photomicrography system from Jenoptik, a cooled CCD camera with a software package called ProgRes. It did what I needed, which was basically to provide an easy way for students to see on the computer screen what they were looking at on the microscope, and also to capture time lapse recordings of developing embryos. It had other useful features, like being able to calibrate the images, automatically annotate them with scale bars, etc. I had quite a few students learning how to easily get scientific-grade images out of this thing.
“Had”. The system has a few huge flaws: like most of the companies making these gadgets, the scientific side feels like a low-profit sideline for them, and most of the money is coming out of industrial imaging applications. That means poor support for us people who are on a tight budget who aren’t going to buy a hundred cameras for our factory, and that means you’re screwed when something doesn’t work. The software for this system breaks every time there’s an update to the MacOS. Like, it runs, but it doesn’t connect to the camera, so all I see is a blank screen. And the software hasn’t seen an update since 2010.
The last time this happened, they sent me a camera firmware patch that had to be run from a PC, not a Mac, and a slightly patched version of the application. It got it working again, but I can see the writing on the wall: as far as Jenoptik is concerned, they are done, they’ll continue to sell off their inventory as long as suckers are willing to buy it, but it’s not as if they’re going to invest any further resources into maintenance and development for mere biologists. It’s frustrating. The system is currently dead and useless.
So I’ve been exploring alternatives…on a tight budget. I’ve come to the conclusion that simple consumer grade cameras are far better bang for the buck. They won’t work if you’ve got some specific, narrow application, like low-light fluorescence imaging, but for the kind of general transmitted light microscopy I do, they’re better: higher resolution, more control, more imaging options. The only thing they lack is that one touch of a button capture of an annotated image.
I was tinkering this morning. Canon Rebel cameras come with something called the EOS Utility, which allows you to connect the camera with a USB cable (or in some models, over wifi) and control everything — aperture, exposure, focus, ISO, I mean everything, and take pictures with a click of a button. You can also set it up to do time lapse with intervals as short as 5 seconds (my usual is one image every 60 seconds, so no problem), and it was impressive to watch. It takes a photo, downloads it to the computer, and shows a preview image, and you end up with a folder of 30mbyte RAW images, which is just what my camera is set to take, I could go to a lower resolution. I’ve got tools to convert those to mp4s, and I also have tools to do bulk processing.
It’s somewhat more complex than a dedicated software solution, but I have smart students. They can master this easily. And the output is much nicer.
Now the next step: paying for this. Anybody want to buy a Jenoptik C3 camera? I can’t use it anymore, but maybe they’ll be better about keeping it updated for Windows machines. Otherwise, it’s going to get stuffed in a drawer and forgotten.
I can get a Canon t5i body (I don’t need lenses) for a few hundred dollars, and even the nice t7i for a bit more, and I’m happy with used cameras, too. It’s about a fifth of the cost of my Jenoptik! I may have to write an in-house grant proposal to scrape up that much, or if there’s anybody out there that has an old Canon sitting in a closet, I’ll take it off your hands. I’ll even put a label on it naming it after you: the [your name] Spider Cam! What an honor! I know some companies would dream of this promotional opportunity, but I’m sorry, I won’t accept the Exxon Spider Cam or the Facebook Spider Cam. I do have limits.
Until I can set up a dedicated lab camera, though, I’ll make do with my personal camera. If anyone out there is setting up a lab and need a low-cost camera system, I’ll offer a word of advice: steer clear of Jenoptik.
I have a canon 5dmk2 that has a busted lens. If you’ll give it a good home I’ll donate it. It’s been around the world several times and is a very cosmopolitan camera.
Oh wait. It also has a busted USB interface.
I would look into the Canon 90D, even if you have to buy it used as it’s an $1,100 body (but Canon takes trade ins and has rebates all the time). It’s a crop sensor (better for macro) and will work with your lenses, but it’s one of two Canon cameras with build in focus stacking. They call it focus bracketing, but the camera will do all the minute focusing work and send all the images over wifi to combine them.
Before you go and do something drastic like spend money on a solution, check and see if anyone has written the required bits to connect your existing, perfectly good camera to micromanager. imageJ keeps itself pretty well up to date and has a pretty supportive community overall, no profit margins screwing with priorities.
Yeah, lenses are irrelevant, but the USB is essential.
The 90D is great, but we’re talking about budget photography here.
Don’t underestimate the value of not having to learn how to use equipment. A good interface can be worth as much as good technical specs, if not more.
My first idea would be to stop updating the OS. Install a bluetooth adapter if needed (transfer to phone) and keep it off network. Backup a working system to image just in case.
The USB interfaces on the MK2 are just soldered to the mainboard. A German border cop yanked it out of the bag and didn’t notice there was a cable plugged in until the housing came apart. Canon wanted more than the camera is worth to fix it (i.e: how to fix it is but a MK3!)
The interface on the Jenoptik system isn’t that great. Like I said, I’ve got smart students.
I can’t help wondering there is Linux software that will support the Jenoptik…and if it could be run on a Raspberry Pi. That would replace getting a (relatively) cheap camera with an actually cheap computer. The current top of the line Pi ought to be able to handle anything the camera can throw at it.
If you think support for industrial products is any better, you are mistaken. I can’t speak about Jenoptik as such, but my experience with industrial control and interfacing systems has shown me that it’s like that and worse everywhere. What mostly happens in industrial environments is that they don’t update or change the control systems. I removed the last NT4 machine from a customer of mine just 2 years ago. They have machines using XP here and there. Those industrial systems cost a lot of money, but the companies making and selling them don’t do software well. And the customer isn’t going to buy a new machine (which can cost millions of dollars!) just because the OS on which the driver runs isn’t supported anymore. We isolate those machines and live with them as long as possible. So I would think about keeping a few old Macs with old MacOS around.
And consumer stuff isn’t THAT much better. What tells you that interface driver or nice Canon software will run on MacOS 10.20? The camera will still work, but they’ll want to sell you a new one with new software before then.
Great idea. I have the t5i and am familiar with the software that you describe. The folks at photomicrography.net can explain how to mount it to a microscope if you need any advice about that.
You might also want to check out Helicon Remote software: https://www.heliconsoft.com/heliconsoft-products/helicon-remote . It does some fairly flexible time lapse (like combining time lapse and exposure bracketing) as well as straightforward remote capture. We’ve been happy with it as a microscopy photo platform, including student use. We happen to use it with a Nikon body, but they support Canons, too.
It also talks nicely to their companion product, Helicon Focus, which does focus stacking. Note that you don’t necessarily need complicated rails or servo-controllers for focus stacking. We just use Helicon Remote to shoot a series of pictures as we manually move the microscope focus through the object.
Why not buy few ocular adapters ( ~$150 last time I checked) and 3D print a few cell phone mounts? Current cell phone cmos chips are excellent and many are sensitive enough to record bright fluorescence. You may not even need the ocular adapter lenses. Then it’s about 3 bucks a scope.
Of course, FIJI for annotations and analysis.
My scopes are all fitted with trinocs, and I have adapters for Canon and Nikon — using a cell phone would be a step backwards.
Depending on your application, it might not be. Granted, a decent SLR will produce better images. However, I had a colleague who wanted to film zebrafish hearts beating. His scope was adapted for an (admittedly lower- midrange turnkey system from one of the microscope Big Four). We tried several of the company’s microscopy-specific cameras ( in the 5k-10k range) and nothing could touch a decent cell phone. Our undergrads use perfectly decent cmos cameras from a lesser know company. They come bundled with a workable capture/analysis suite, but the fact is, cell phones work better for picture quality on the cheap. Obviously, where sCMOS or EMCCD cameras are required; they’re required, but for quality on the cheap (which is the challenge with UG labs for sure), you can’t beat the cell phone option. I’ve tried. Except for moderately (or more) demanding fluorescence applications or where high temporal resolution is necessary, generating publication quality images with the setup I’m describing is easy. And of course very cheap. The autofocus function allows most phones to be used in the trinoc port as well, if you don’t want to tie up an ocular. Anyway, that’s my experience.
Maybe you’ve tried this already, PZ, but would running Windows in a virtual machine on your Mac let you use the software?
I’ve been shooting nice insect images with my Nikon D700 and macro lenses using Capture One software to control the camera through an iMac. That software is easy to use and can control all the parameters and settings of the camera through the iMac. They even have a student price so get a student to sign up for it. A free trial is available to download and test drive. http://www.captureone.com
(FAQ Jenoptik)
.. but it seems it does have a Linux SDK.
… and there are people claiming to do C3+ImageJ?
Hmm …
… that’s neither here nor there …
As Sean Boyd mentioned virtual machines are occasionally an absolute SkyFairysend.
I’m currently using Parallels on a Catalina OS so that I can continue to use Fontographer on Mojave!
I’ve received official email from Jenoptik. My camera has been discontinued and will no longer be supported. They also don’t support any MacOS version after 10.12.
Well, that makes it easy. I’m done with them, the camera is going to get shelved somewhere and never used again.
The Canon EOS Utility is OK but the Backyard EOS from O’Telescope is far more powerful for camera control and image programming.
https://www.otelescope.com/files/
Works with both USB and wi-fi, and lets you save your images to the camera chip and/or to your hard drive. You can set up and save complex image programs and run them later, and the program stores a log of all of your shots. Custom file names too.
Free 30-day trial and the full package is a big $50.00.
I use my copy with my Canon for astrophotograpy, but an optical tube is an optical tube.
Backyard is not MacOS compatible, unfortunately.
I hate to say it, but if you want to limit yourself strictly to MacOS, you’re making things harder for yourself. As someone mentioned above, you could run Windows 10 in a VM on the Mac and open up your options considerably.
I’ve used GB Timelapse from Granite Bay Software (gbtimelapse.com) and it provides excellent control for Canon cameras…on Windows.
Another vote for just not updating the OS. Set aside an old computer to run the thing, with a sufficiently old version of the OS, and never touch it again.
Yes, that’s how it works in industry too. I’m a bioinformatician with a specialty in image analysis / high content screening. I’ve had some adventures. I once had to literally hide a computer to protect it from the IT department, who were trying to confiscate it as a security hazard. (We told them we’d gotten rid of it, but we’d just taken it off the company network. There was a decoy computer of current vintage placed next to the instrument; it was set up to retrieve data from the hidden computer and pass it along.) Another group let IT push updates to their machines…until the auto-update from Windows 7 to 10 turned their microscope into a $500K paperweight. It’s not paranoia; the updates are actually out to get you.
PZ,
I’ve got a T1i you can have if you want it.
Everything works. Some coke got spilled on the top and if you want the flash you have to press the flash release and help it up. Professional cleaning would probably clear that up. I just replaced it with a T5i.
When I go for the T7i or T8i I’ll think of you…