Stacking Workflow

[ray_parkhurst]

My existing rail uses a Trinamic stepper, with USB driver. This system is well-supported by Helicon, which has been my go-to software for stacking control and rendering of the stacked images. I have been very happy with this system as it uses the USB connectivity of my Canon cameras for controlling the camera during the stack. This makes a seamless transition from single-shot use of the Canon EOS utility to the Helicon Remote, though both cannot be run simultaneously.

Recently, I've been dabbling in a couple of systems sourced from sellers who are members of this forum: wemacro and mjkzz. From what I understand, their systems are meant to emulate the functionality of the Stackshot. Unfortunately, coming from the Helicon / Trinamic side, I am a bit in the dark about how to best use these systems, and hence the reason for this post.

My most recent work has been with the mjkzz system, so that's where I will start. Another reason for starting here is that Peter graciously sent me a Voice Coil controller to beta test, so the workflow with that controller is of strong interest. What I'm finding is the workflow for this system is much different from the Helicon/Trinamic system with Canon camera.
The mjkzz system is a USB-based controller and software similar to the Helicon Remote system, but the camera control is via separate shutter release cable. I am able to use Live View via USB/EOS Utility to set the start and stop points, but with the USB connected the shutter release is disabled such that shutter release during a stack won't function. When I disconnect the USB, the camera will drop out of Live View, so I have to go to the camera and press Live View before starting a stack. This all seems very onerous.

Is this functionality similar to the Stackshot? How do folks using the Stackshot (or mjkzz or wemacro) systems when setting up the stack start / stop view the object on-screen? I can see potentially using the HDMI output, but then I could not view the controls on the screen to set the limits. Does everyone have a dual-monitor system? Do you all use the puny camera screen to set limits? Do you all have to mess with the camera before each stack to put it into Live View mode?

So far this workflow issue the most severe limitation (for me) to both the wemacro and mjkzz systems, and possibly also the Stackshot. Please let me know how you guys are using the Stackshot/wemacro/mjkzz systems to view and set limits and initiate the stack, start Live View, etc.

Finally, if I un-plug the USB to allow the wemacro/mjkzz (and I assume Stackshot) systems to trigger the shutter, I have to then plug in the USB again to download the images. I'm loathe to plug and unplug the USB so often as they wear out eventually. I suppose I could use a USB switch to connect? Perhaps I am just spoiled that the stack images download automatically via USB, and by Helicon Remote's automatic opening of Live View.

Is all of this solved by using Zerene for Stackshot? What about the wemacro / mjkzz systems?

[rjlittlefield]

Is all of this solved by using Zerene for Stackshot?

Take a careful read through the "Recipes" at https://www.zerenesystems.com/cms/stack ... /stackshot to see how things work with that combo.

I suspect the bit you need to know is at step 9 in the Canon recipe:

Press Live View button on camera so as to make the camera display the Live View image on its own monitor. (This is important. If the camera is in Live View mode but is not displaying the Live View image by itself, then the camera will ignore shutter commands coming from the StackShot.)

--Rik

[austrokiwi1]

I can't address all your questions. I will just cover what I have experienced and my experience is different as I am a mirror-less user.
I use stackshot and zerene. I have used Helicon but abandoned it.
I have tethered, the Sony A7rII ( using Capture one pro) and have used the Zerene controller in conjunction with tethering and the stackshot. I have also used a separate HMDI monitor. In the end with the sony I find the simplest workflow is to actually use the A7rIIs rear monitor and the stackshot controller The reasons being:
1. Although small the cameras monitor is of higher resolution than my laptops screen or the separate HMDI monitor. With the rear monitor of the sony A7rII what you see in the cameras monitor( or even better the electronic view finder) is what you get ( no need for the histogram)
2. Focus peaking makes setting start and end points for stacks extremely quick and easy. With the usual magnification range for coins focus peaking means there is no need to use either the cameras manual focus magnification aid or the similar aid in Capture one 10 (when tethered). I would anticipate that magnifications of 15X and higher, focus peaking would not be so useful.
3. Focus peaking is also available on the separate HMDI monitor but it is no where near the performance of the cameras focus peaking
4. As I noted earlier as what you see in the cameras view finder (or monitor) is what you get, the Histogram is mostly, if not completely, redundant. On the odd occasion that I need to make finer adjustments to the exposure I resort to using the zebra feature. It is much more intuitive than a histogram.

The only good thing about tethering is that the photos are loaded straight into Capture one pro for editing. However, even that is a marginal advantage. I have recently built a PC for image editing. With this build I have found it is simpler to transfer the photos from the cameras sd card. 64GB ram, an overclocked system and a solid state working drive (boot drive is M.2 Nvme) see's lightning fast file transfers, a 200 shot stack takes less than 3 minutes to transfer from the SD card (via USB 3.1 connected internal card reader). Note each 14bit raw picture is 128 mb in size.

I would actually like to know how Lou would answer your questions in relation to his Pen F and the inbuilt stacking( I am not impressed with that feature on my Oly OMD-Em10II)

[/list]

[ray_parkhurst]

Is all of this solved by using Zerene for Stackshot?

Take a careful read through the "Recipes" at https://www.zerenesystems.com/cms/stack ... /stackshot to see how things work with that combo.

I suspect the bit you need to know is at step 9 in the Canon recipe:

Press Live View button on camera so as to make the camera display the Live View image on its own monitor. (This is important. If the camera is in Live View mode but is not displaying the Live View image by itself, then the camera will ignore shutter commands coming from the StackShot.)

--Rik

Hah! Wonderful, thank you Rik. Works like a charm. I just have to press the LV button once right before starting the stack.

I will sleep better tonight.

[Lou Jost]

Austrokiwi, I am a big fan of the focus-bracketing function of the PEN F, especially when I can use continuous light. The workflow couldn't be any simpler. A 200 image stack takes a minute or two to capture. The in-camera peaking makes it easy to set a starting point without an external monitor, though I do find an external monitor to be useful to make sure nothing important is left out of the stack. I trigger the shutter and let the stack run until I am sure I've passed the part of interest; a second shutter press stops it. The screen stays on during the whole process so you see exactly what is happening. I then take the card out and process normally in Zerene.

When I have a high volume of photographic work that needs to get done fast, there is nothing better than this. The limitation is that it cannot easily be applied to microscope objectives. But with my home-built automatic reversing ring, I can use it with reversed MFT lenses to achieve higher magnifications. I can confirm that everything works well at 2x and I suspect slightly higher m is possible.

When I am really rushed I don't even mount the camera, just lay it (lens facing down) on a stereo microscope focusing stand (in place of the microscope head) and slide it around and use the microscope focusing dial if needed, to compose and focus my initial shot. Flexible and fast.

[Lou Jost]

I should add that WeMacro has a new rail and controller, which is on its way to me here in Ecuador as we speak, so I may have some news to add soon about stacking by rail, which is the method I use when microscope objectives are needed.

[ray_parkhurst]

I have a rail from wemacro, and it works pretty well. If I had known the trick of pressing the Live View button on camera to activate remote shutter operation I might never have gone down the path I am currently on. I ended up converting a KR26 rail to a vertical setup using a mjkzz kit and a lot of pre-cut aluminum from eBay. I built the system up before I realized I had the same problem with it that I had earlier with the wemacro rail! Luckily there is a trick to it, and now I'm fully functional, with both the KR26 rail stepper and the voice coil stepper on the same vertical system. I'll take some pics with it and of it a bit later to share.

I ended up also buying a KR20, and am trying to figure out what to do with it. It's too short to do the same type of rig as the KR26. I'm thinking of something a bit different for it. Anyone else built a stacking rig out of the KR20?

[austrokiwi1]

Lou, does the PEN F tether?

[Lou Jost]

It has an HDMI-out port for streaming the live view at good resolution, and a micro USB port for connecting to Stackshot or WeMacro controller or camera control programs (which I very rarely use).

Edited to remove the phrase "USB-out port" since it is of course a two-way communication channel.

[Lou Jost]

One other workflow observation:The fastest way to process multiple stacks is to do them simultaneously in multiple instances of Zerene, as Rik noted somewhere. It is faster to do two or three stacks in Zerene simultaneously than it is to do them in series, though on my computer, four or more instances of Zerene running at the same time will cause performance problems and sometimes crashes.

[mawyatt]

Ray, Lou,

I have the THK KR20 with Peter's kit I use with a Stackshot controller with a adapter cable I made (made one for the WeMacro and Peter's rails also). The KR20 has a 1mm/rotation screw thread and I use a 400 step motor, so basic step size is 2.5 microns before engaging micro-stepping. Also have WeMacro, and Peter's SR-90 rails as well as a very old Stackshot. I like this setup because I can use Zerene to control the stage, whether it's a Stackshot, KR20, WeMacro or SR-90, without having to worry about any scaling factors as Zerene allows rail details to be recorded and used with whichever rail is in use.

I use a Nikon D500 or D800E camera body with a remote HDMI monitor, and just pull the card to transfer the files into Zerene on a Mac Pro. May not be the quickest or best, but this works for me. The D500 has electronic front curtain which I use, the D800E does not. All files are recorded in camera as TIFF files, so no conversion from RAW is necessary. Normally don't worry too much about precise start and stop points, just make sure that the two ends are covered. I remove the out of focus before start and end files in Zerene before stacking.

I don't do a bunch of stacks at the same time, usually just relative long (200~400) single stacks, so my workflow may be different.


Best,

Mike

[Lou Jost]

Mike, I also just pull the card to get images into my computer.

I always shoot RAW + jpg and generally just stack the jpgs unless it is something important. For images that will be published, the ability to get the exposure just right in RAW is very important to me, as well as the ability to completely control the strength and timing (before vs after stacking) of the sharpening algorithm. I think this latter flexibility is very important.

I almost always use the completely silent fully electronic shutter, which is vibrationless. In the PEN F it works even with flash, unlike almost all other cameras.

My stacks tend to be shorter than yours. Mike, and if I am doing focus-bracketing, I am often producing large numbers of stacks, very fast (theoretically under continuous light I could shoot thousands of photos per hour under this workflow, though in reality I only shoot a few hundred per hour ), so the computer is the bottleneck. One reason I like the fully electronic shutter is that at this rate of shutter release, a mechanical shutter would die quickly.

[ray_parkhurst]

The workflow using the LV trick has pros and cons vs my previous one:

Pros:
- no need to open separate program to control the camera. Before I had to close EOS utility and open Helicon Remote since they competed for camera control
- keeping EOS utility open allows use of the rail for single-shot focusing
- maintain the USB connectivity for auto file downloading into DPP

Cons
- must do the trick of pushing LV before a stack, meaning I must physically go to the camera, so it can't be too remote
- must do a "pre-shot" before starting the stack because first shot after turning on camera opens DPP and obscures EOS window.

The pros significantly outweigh the cons so this is a big win. I suppose this is how I would have done stacking all along if I had used a Stackshot.

The vertical system I built is much more solid than my previous one. Even at 10x in zoom view there is an absolute minimum of movement on shutter release, and it damps in ~100msec. This seems to result in a more consistent sharpness to the stack, actually best I've seen with this equipment.

The KR26 has 2mm pitch, so with 400 step motor has full-step resolution of 5um, well within my needs for 5x or 10x. At 20x and above I can use the Voice Coil motor. I don't really use anything above 10x for coins, but I do for other things like phonograph stylus evaluation, etc.

Here is an RPM Lincoln Cent using the 10xMM objective:



edited to add a perspective rendering. This is probably the sharpest rendering, with best rendering of feature-edge detail, at 10x I've acheived...

[austrokiwi1]

I am quite perplexed by this focus on work flow. I can understand that if someones business/work involved taking macro photographs all day long( for example a coin auction house taking photographs for their latest sale) in that case analyzing the work flow would be of great importance. However in a life sciences laboratory where macro/micro photography is only an infrequent activity,even if on a daily basis, I can not see any advantage in focusing on the work flow.

So My question is why the emphasis on work flow?

[Chris S.]

Lou,

. . . though on my computer, four or more instances of Zerene running at the same time will cause performance problems and sometimes crashes.

. . .I am often producing large numbers of stacks, very fast . . . . so the computer is the bottleneck.

If you’re interested in easing this bottleneck, I can just about guarantee that these crashes are the result of the computer’s becoming too hot. It’s straightforward to increase the rate of heat flow out of a computer, if you’d like to discuss it.

In terms of performance problems when running multiple instances of Zerene Stacker, my first thought is to build an efficient machine with eight cores, and dedicate it to stacking. In the case of a dedicated stacking machine, concurrent performance for other tasks isn’t very important. (This said, would also want to ask Rik if there is any benefit in assigning individual instances of Zerene Stacker affinities to specific cores. But I’ve found that a sufficiently powerful PC can easily handle multiple Zerene Stacker jobs without compromise to other work.

In my workflow, an older, lower-powered laptop controls image acquisition—displaying live view, controlling camera via tethering, collecting images from camera, and sending these images over wireless network to a much more powerful tower PC, which runs the stacks under Zerene Stacker.

In a former workflow, the stacking computer then sent stacks to another computer, on which I did final work in Photoshop. But as said, I now find that a single, powerful tower PC is convenient for stacking several images at once, retouching them as necessary, performing post in Photoshop, while doing other work simultaneously.

--Chris

--edited typos