Using video for botanical close-up stacks

A forum to ask questions, post setups, and generally discuss anything having to do with photomacrography and photomicroscopy.

Moderators: rjlittlefield, ChrisR, Chris S., Pau

gardenersassistant
Posts: 190
Joined: Sun May 31, 2009 5:21 am
Location: North Somerset, England

Using video for botanical close-up stacks

Post by gardenersassistant »

In 2016 I experimented briefly with using video to capture/derive images for stacking. This was using Panasonic's post focus facility which captures video as it racks from the front to the back of a scene. At that time I was using 4K videos, some captured using an FZ330 bridge camera with and without a mild close-up lens and some using a G80 micro four thirds camera with an Olympus 60mm macro lens.

After doing some experiments I put it to one side because too often I found it too difficult and time-consuming, or in some cases impossible, to deal with artefacts that spoilt the stacks. There were various issues, including noisy backgrounds, posterised backgrounds, and halos of various sorts. I was using Helicon Focus because it made it very easy to derive source JPEGs from the post-focus videos. To some extent the problems were amenable to retouching from individual source images and/or from alternative stacks.

The issue that occurred often and seemed most intractable arose where there were two elements that I wanted in focus that overlapped but with enough distance between them that there were no images with the area of the rear element in focus where it appeared around the edge of the front element. I discussed this with an example from 21:55 in this video at You Tube.

During 2017 I returned to this technique to try it again a small number of times with the G80, but although I got a few results I really liked the failure rate discouraged me greatly. However, as 2018 progressed I used the technique more and things improved. I think this was probably a combination of getting a bit better at choosing suitable scenes for stacking coupled with exploring and slowly getting better at using the options that Helicon Focus offered.

In 2016 and 2017 I also dipped into focus bracketing. The problem I found with that, for my purposes, was that the capture rate was rather slow, at around 4.5 frames per second. I live in a notoriously breezy location and waiting for a calm day is not a practical solution, which means that I was often working in a breeze, trying to capture the images for a stack in brief lulls in the breeze when the plants were not moving around so much. I also preferred to work hand-held because of the flexibility this gave me. In these conditions the 30 frames per second of post focus capture is a significant advantage.

A disadvantage of post focus is of course is that you are using JPEGs. With focus bracketing I could use raw. However, the buffer on the G80 fills at between 40 and 50 captures, from which time the captures become very slow. My stacks involved more than 50 images often enough that I moved to JPEGs for focus bracketing, which didn't suffer from the buffer issue. However, the capture rate was still no faster than for the (pre-full buffer) raw captures. I quite soon moved to using post focus exclusively, and as the year went on used post focus stacking a bit more often and became more comfortable with it.

Mostly though I was still shooting single images for botanical subjects. For this I took to using aperture bracketing, getting a series of shots from f/2.8 to f/22 with each press of the shutter button. This let me work fast and flexibly out in the field while giving me as much time as I wanted during post processing to pick the one (or occasionally more than one) I thought had the most pleasing balance between focus coverage of the subject and the rendition of the background.

Last autumn I had a brief full frame interlude. I wanted to see if I could get botanical images I liked better using a full frame camera, and so I bought a Sony A7ii on which there was a very good cashback offer. With no focus bracketing or post focus on the A7ii I was working exclusively with single image captures and it quite quickly became apparent that this was not going to give me the images I had hoped for. I decided instead to do the only thing I could think of, in terms of equipment, to possibly improve my botanical imaging, especially including close-up stacking, which was to go upmarket to a Panasonic G9. This had a few more megapixels, 20 vs 16 for the G80, apparently had an extra stop of dynamic range and allegedly produced better JPEGs. It also did (18 megapixel) 6K rather than (8 megapixel) 4K video. I thought some or all of these improvements might help a bit.

There turned out to be some benefits that I had not registered beforehand. One was that the G9 has an extremely configurable button, wheel and joystick setup which turns out to work very well indeed for my botanical activity. Another is that it lets me use a rather flat Cinelike D profile, which helps with dynamic range. I have also turned the noise reduction and sharpening to their minimum settings so as to improve the processing latitude. And for that other JPEG issue, white balance, I have the camera set up so it is extremely easy and quick to set the white balance (from the grey panel on a ColorChecker Passport), for each scene if I want.

Best of all, the rendition of colours and textures meets the approval of my wife. She is not a photographer but is very good with colours and she knows her plants very well. Over the past decade since I have been photographing her plants she has been commenting about how the colours are often not right. Of the current setup (she just looked over my shoulder at this post) she said "tell them your very picky wife gives it 10 out of 10 for colours and the way it captures textures.". She said the images capture the richness and subtleties she sees out in the garden without, as in her view all my previous images have done, over-hyping the colours. And she is entirely content with the additional expenditure on (yet more) kit. :D

As far as capture technique goes, I have started using a tripod again. I have an extremely flexible tripod which I used a lot 3 and 4 years ago, but stopped using for a couple of years. I am using it hands-on, much as others use a pole or monopod to dampen hand-shake while still retaining a fair degree of flexibility and speed of deployment.

The upshot of all this is that, given the results I am now starting to get with greater frequency, I am finding myself drawn increasingly to stacking for botanical subject matter, to the extent that I'm now having sessions when I don't do any single-image captures at all. My enthusiasm for it extends to contemplating some experiments with a somewhat similar approach for invertebrates. I currently use a minimum aperture approach (f/45 full frame equivalent) most of the time for invertebrates, whether with (most of the time) 1/2.3" or (more in the past than currently) with micro four thirds or (several years ago) APS-C (all three with close-up lenses and a Venus Optics KX800 twin flash). When the invertebrates return next season I intend to try post focus stacking for invertebrates with the FZ330 and (mainly) Raynox 150 close-up lens, with a diffused LED light.

Here are half a dozen examples of botanical stacks using my latest (still in early testing, development and familiarisation) approach using the G9 in our garden since Christmas Eve. After stacking and retouching in Helicon Focus they were finished in Lightroom. There are 1400 pixel high versions at Flickr.

#1 Hebe. 27 frames stacked, f/2.8, 1/125 sec, ISO 800, -0.3EV
Image
1417 02 2018_12_24 P1001204 G9+60 PF27f F2.8 1-125 ISO800 -0.3EV B8,3+i LR7 1400h by gardenersassistant, on Flickr

#2 Formium. 55 frames stacked, f/2.8, 1/125 sec, ISO 200, -0.7EV
Image
1417 09 2018_12_24 P1001250 G9+60 PF55f F2.8 1-125 ISO200 -0.7EV B33,2+cl LR7 1400h by gardenersassistant, on Flickr

#3 Rue. 97 frames stacked, f/2.8, 1/160 sec, ISO 400, -0.3EV
Image
1417 10 2018_12_24 P1001258 G9+60 PF97f F2.8 1-160 ISO400 -0.3EV C2 LR7 1400h by gardenersassistant, on Flickr

#4 Hypericum. 61 frames stacked, f/2.8, 1/80 sec, ISO 800, -0.7EV
Image
1417 20 2018_12_24 P1001357 G9+60 PF61f F2.8 1-80 ISO800 -0.7EV B9,3 LR7 1400h by gardenersassistant, on Flickr

#5 Fern. 27 frames stacked, f/2.8, 1/80 sec, ISO 800, -0.7EV
Image
1417 21 2018_12_24 P1001367 G9+60 PF27f F2.8 1-80 ISO800 -0.7EV B9,3+i LR7 1400h by gardenersassistant, on Flickr

#6 Rose hip. 46 frames stacked, f/2.8, 1/500 sec, ISO 800, 0EV
Image
1421 03 2019-01-01 P1001480 G9+60 PF46f F2.8 ISO800 1-500 0EV B9,3+B9,3(57f) LR7 1400h by gardenersassistant, on Flickr
Nick

Flickr
Blog
Journey since 2007

Rework and reposts of my images posted in this forum are always welcome, especially if they come with an explanation of what you did and how you did it.

RDolz
Posts: 96
Joined: Mon Aug 28, 2017 9:32 am
Location: Valencia (Spain)

Post by RDolz »

Nick:

Congratulations, a continued effort that has given its "fruits".
It is not immediate to debug a technique and get such good results (without doubt, G9 has been a good choice) I hope the invertebrates arrive soon and see your images! :smt038
Ramón Dolz

Troels
Posts: 600
Joined: Mon Feb 15, 2016 11:06 am
Location: Denmark, Engesvang
Contact:

Post by Troels »

Very nice pictures with wonderfull light and colors.
Troels Holm, biologist (retired), environmentalist, amateur photographer.
Visit my Flickr albums

TheDocAUS
Posts: 110
Joined: Thu Jul 19, 2018 10:44 pm
Location: Sydney

Post by TheDocAUS »

Nick

Great work. I am learning a lot from your postings.

What model is the Model No of the Benro? I just use a normal tripod with a 3 way geared head from Sunwayfoto. https://sunwayfoto.com.au/product/sunwa ... 7-version/

gardenersassistant
Posts: 190
Joined: Sun May 31, 2009 5:21 am
Location: North Somerset, England

Post by gardenersassistant »

RDolz wrote:Nick:

Congratulations, a continued effort that has given its "fruits".
It is not immediate to debug a technique and get such good results (without doubt, G9 has been a good choice) I hope the invertebrates arrive soon and see your images! :smt038
Thanks. Yes, it is taking some time to understand better how to use it (but then again I'm a bit slow on the uptake, so others may well get there much faster than me.)

I'm very pleased indeed with the G9 (although this is all I'm using it for so I don't know what it is like for other things - it seems pretty good though from what I've read.)

Invertebrates - the sooner the better! But it could be a while yet. :(
Nick

Flickr
Blog
Journey since 2007

Rework and reposts of my images posted in this forum are always welcome, especially if they come with an explanation of what you did and how you did it.

gardenersassistant
Posts: 190
Joined: Sun May 31, 2009 5:21 am
Location: North Somerset, England

Post by gardenersassistant »

Troels wrote:Very nice pictures with wonderfull light and colors.
Thanks. It has been a bit of a surprise how they have come out, not so much in how they look (which is pleasing of course), but in the sense of how little I have had to do to them to get them there. Given the flat profile, and turning the noise reduction and sharpening right down, I expected to have to work on them a bit more than usual. However, for many of them I have simply been adjusting the lightness a little (or not at all), with sometimes a soft touch on the highlights and/or blacks. So in fact simpler than usual. Actually I'm a bit puzzled by that as to why that should be.

Apart from these "baseline" adjustments, just some cosmetic stuff that I would be doing anyway like cropping, occasional minor cloning to remove background annoyances or graduated/radial filters to do local brightness balancing.
Nick

Flickr
Blog
Journey since 2007

Rework and reposts of my images posted in this forum are always welcome, especially if they come with an explanation of what you did and how you did it.

gardenersassistant
Posts: 190
Joined: Sun May 31, 2009 5:21 am
Location: North Somerset, England

Post by gardenersassistant »

TheDocAUS wrote:Nick

Great work. I am learning a lot from your postings.

What model is the Model No of the Benro? I just use a normal tripod with a 3 way geared head from Sunwayfoto. https://sunwayfoto.com.au/product/sunwa ... 7-version/
Thanks. I'm glad you like the text. My stuff goes on too much for some people. :)

It is a Benro Flexpod C2980F Versatile Tripod Carbon Black. I see that it is currently unavailable at Amazon UK and only available used at Amazon.com, so presumably it isn't made any more. However, anything with a reversible central column would do. The thing that gives it the extra versatility is the arm, a Velbon V4 Boom Arm.
Nick

Flickr
Blog
Journey since 2007

Rework and reposts of my images posted in this forum are always welcome, especially if they come with an explanation of what you did and how you did it.

palea
Posts: 40
Joined: Mon Dec 17, 2018 8:09 pm

Re: Using video for botanical close-up stacks

Post by palea »

Benro currently offers 180 degree columns on their Go Pro models and Vanguard on their Alta Pros. The other main 180 degree option I'm aware of is the now discontinued Gitzo Explorers. Benro and Manfrotto both offer fixed 90 degree columns in their Go series. There are also scattered models from other manufacturers with column mountings besides reversing. A less capable but less involved, loosely equivalent option is use of a nodal slide or long Arca rail. As magnifications approach or exceed 1x I've found there's compromise to all of these options in tripod stability and therefore to ease of positioning and how much handling sets up vibrations. There's not exactly a large set of better alternatives in the field, though.
gardenersassistant wrote:[the G9] lets me use a rather flat Cinelike D profile
Interesting observation. Checking the manuals, Cinelike D is available on the G80/81/85 and earlier but is restricted to the creative video mode. Seems somewhat arbitrary on Panasonic's part.

gardenersassistant
Posts: 190
Joined: Sun May 31, 2009 5:21 am
Location: North Somerset, England

Re: Using video for botanical close-up stacks

Post by gardenersassistant »

palea wrote:Benro currently offers 180 degree columns on their Go Pro models and Vanguard on their Alta Pros.
Thanks. The GoPlus range has me interested. They have improved the column adjustment. I would generally want it either upright or upside down rather than at intermediate angles, but reversing it from upright to upside down looks like it would be much easier. At the moment I have to take the central column out and reinsert it the other way round, which is awkward with the secondary arm and camera attached. The new mechanism looks like reversing would be much simpler and quicker.
palea wrote:The other main 180 degree option I'm aware of is the now discontinued Gitzo Explorers. Benro and Manfrotto both offer fixed 90 degree columns in their Go series. There are also scattered models from other manufacturers with column mountings besides reversing. A less capable but less involved, loosely equivalent option is use of a nodal slide or long Arca rail. As magnifications approach or exceed 1x I've found there's compromise to all of these options in tripod stability and therefore to ease of positioning and how much handling sets up vibrations.
Indeed so, although vibrations are not an issue for my usage as I generally use the tripod hands-on, also meaning that instability isn't an issue for me. To get at awkwardly positioned subjects I quite often use it in unstable positions that couldn't be used hands-off, including using it sometimes with one or occasionally two legs off the ground.
Nick

Flickr
Blog
Journey since 2007

Rework and reposts of my images posted in this forum are always welcome, especially if they come with an explanation of what you did and how you did it.

user6672
Posts: 5
Joined: Sun Sep 09, 2018 3:56 pm

Post by user6672 »

Are these done with the G9's post-focus feature, or with some other built-in feature, or "manually"?

gardenersassistant
Posts: 190
Joined: Sun May 31, 2009 5:21 am
Location: North Somerset, England

Post by gardenersassistant »

user6672 wrote:Are these done with the G9's post-focus feature, or with some other built-in feature, or "manually"?
With the G9 I use post focus to capture 6K MP4 videos, several for each scene. On the PC I use Panasonic's PhotoFun Studio to quickly review the videos of a scene and choose which one to use. I drag the video into Helicon Focus which automatically extracts JPEGs and aligns them. I then select which of the JPEGs to use. stack them and when necessary retouch the stacked image with individual source JPEGs and/or with an alternative stack which used different stacking parameters and/or (occasionally) cloning. I then get Helicon Focus to produce a TIFF file which I import into Lightroom to finish the image and produce a JPEG. Very occasionally I do a round trip from Lightroom to Photoshop and back before producing the JPEG.

It is similar with my G80 which I previously used for this sort of botanical scene, but using 4K rather than 6K.

It is similar too with my FZ330 bridge camera, but I haven't used that much for botanical scenes. However, I will probably use the FZ330 to experiment with this technique for invertebrates, which it may do better than the micro four thirds cameras. (The FZ330 with close-up lenses is my preferred setup for single-image captures of medium sized invertebrates using flash. For stacking I will be using the FZ330 with an LED light.)
Nick

Flickr
Blog
Journey since 2007

Rework and reposts of my images posted in this forum are always welcome, especially if they come with an explanation of what you did and how you did it.

user6672
Posts: 5
Joined: Sun Sep 09, 2018 3:56 pm

Post by user6672 »

gardenersassistant wrote:
user6672 wrote:Are these done with the G9's post-focus feature, or with some other built-in feature, or "manually"?
With the G9 I use post focus to capture 6K MP4 videos, several for each scene. On the PC I use Panasonic's PhotoFun Studio to quickly review the videos of a scene and choose which one to use. I drag the video into Helicon Focus which automatically extracts JPEGs and aligns them. I then select which of the JPEGs to use. stack them and when necessary retouch the stacked image with individual source JPEGs and/or with an alternative stack which used different stacking parameters and/or (occasionally) cloning. I then get Helicon Focus to produce a TIFF file which I import into Lightroom to finish the image and produce a JPEG. Very occasionally I do a round trip from Lightroom to Photoshop and back before producing the JPEG.

It is similar with my G80 which I previously used for this sort of botanical scene, but using 4K rather than 6K.

It is similar too with my FZ330 bridge camera, but I haven't used that much for botanical scenes. However, I will probably use the FZ330 to experiment with this technique for invertebrates, which it may do better than the micro four thirds cameras. (The FZ330 with close-up lenses is my preferred setup for single-image captures of medium sized invertebrates using flash. For stacking I will be using the FZ330 with an LED light.)
Excellent, thank you.

Does the G9 automatically decide how many images to take, or do you set the focus locations, or set the number of images or something else?

gardenersassistant
Posts: 190
Joined: Sun May 31, 2009 5:21 am
Location: North Somerset, England

Post by gardenersassistant »

user6672 wrote:
gardenersassistant wrote:
user6672 wrote:Are these done with the G9's post-focus feature, or with some other built-in feature, or "manually"?
With the G9 I use post focus to capture 6K MP4 videos, several for each scene. On the PC I use Panasonic's PhotoFun Studio to quickly review the videos of a scene and choose which one to use. I drag the video into Helicon Focus which automatically extracts JPEGs and aligns them. I then select which of the JPEGs to use. stack them and when necessary retouch the stacked image with individual source JPEGs and/or with an alternative stack which used different stacking parameters and/or (occasionally) cloning. I then get Helicon Focus to produce a TIFF file which I import into Lightroom to finish the image and produce a JPEG. Very occasionally I do a round trip from Lightroom to Photoshop and back before producing the JPEG.

It is similar with my G80 which I previously used for this sort of botanical scene, but using 4K rather than 6K.

It is similar too with my FZ330 bridge camera, but I haven't used that much for botanical scenes. However, I will probably use the FZ330 to experiment with this technique for invertebrates, which it may do better than the micro four thirds cameras. (The FZ330 with close-up lenses is my preferred setup for single-image captures of medium sized invertebrates using flash. For stacking I will be using the FZ330 with an LED light.)
Excellent, thank you.

Does the G9 automatically decide how many images to take, or do you set the focus locations, or set the number of images or something else?
Unlike with focus bracketing, for post focus the camera decides how many images to take. When you half press the shutter button the focus zooms in and out. Presumably the camera is examining the scene to work out how to handle it. When you fully press the shutter button the focus starts around the middle of the focus range and rapidly moves to the nearest thing it can find to focus on. It then moves the focus away fairly slowly (at 30 frames per second, but not far from frame to frame) until it reaches the furthest thing it can focus on. It then returns quickly to the middle.

I think it alters the speed it moves at depending on the aperture. With a smaller aperture the capture is quicker. The capture is often done in two to four seconds, but it can be much longer. I have had one take over 10 seconds, which is over 300 frames. So sometimes I use quite a lot of frames in a stack. For example this one used 201 frames, which is the most I have used for a post focus stack.

Image
1276 06 2018_01_12 G80+60 F2.8 ISO 800 1-500 PF 201f (B,19,1+outer B,19 10)) P1140279LR6 1300h by gardenersassistant, on Flickr

The capture process leaves a (usually, but not always) small number of frames at the start and end of the sequence that are best removed. And of course you may remove more to get the in-focus range how you want it. I generally remove more frames than I keep, although that depends on the scene. Sometimes I have to remove more than I want to and use a narrower focus range than I want because it is the only way to get rid of some particularly intractable halos.

So, post focus is very much a "point and shoot" thing. It takes no (as in zero) time to set up (if you are using a macro lens - it can be a bit more tricky with close-up lenses) and it executes much faster than focus bracketing. This makes for a much more fluid and (for me at least) more creative capturing experience. There are no complications getting in the way and slowing me down.
Nick

Flickr
Blog
Journey since 2007

Rework and reposts of my images posted in this forum are always welcome, especially if they come with an explanation of what you did and how you did it.

BugEZ
Posts: 850
Joined: Sat Mar 26, 2011 7:15 pm
Location: Loves Park Illinois

Post by BugEZ »

Nick,

This is quite interesting. Field stacks have seldom gone well for me but your results here are excellent.

Could you make a demo video of your process? Showing you choosing a subject, setting up tripod and camera, making camera settings and gathering the images. Then back in the lab/home a video sequence of you at your computer pulling the images into the various software packages to create the stack of images, then generating the stacked image.

That would be a great help to me.

Thanks!

Keith

gardenersassistant
Posts: 190
Joined: Sun May 31, 2009 5:21 am
Location: North Somerset, England

Post by gardenersassistant »

BugEZ wrote:Nick,

This is quite interesting. Field stacks have seldom gone well for me but your results here are excellent.

Could you make a demo video of your process? Showing you choosing a subject, setting up tripod and camera, making camera settings and gathering the images. Then back in the lab/home a video sequence of you at your computer pulling the images into the various software packages to create the stack of images, then generating the stacked image.

That would be a great help to me.

Thanks!

Keith
I certainly can do that Keith, although it will take a little while. A couple of caveats though. First, my approach does depend on using Panasonic's post focus. If you are not using a Panasonic camera that has this facility then much of my experience won't be helpful to you. Second, I suspect from your username that you may be interested in insects, spiders etc. Almost all I have done with this stacking has been flowers, buds, berries, seed pods etc. I am intending to have a go at insects etc when they return later in the year, but I don't know how practical it is going to be out in the field, and in fact I am rather doubtful about it. So, if that is your primary area of interest my stacking experience with flowers may be misleading. (Insects etc are my other primary area of interest, but I use single image captures for that, using a somewhat idiosyncratic approach in terms of equipment and technique.)

Anyway, I will make a video. In the meantime here are a couple you might want to look at. The first one is Stacking close ups with Panasonic post focus and Helicon Focus. I made this two years ago after using Helicon Focus for about six hours. My understanding of it was obviously rather limited at that point, but it might be interesting all the same. If you do watch it I would turn the speed up to 1.25X because my delivery was very slow. Also, the references early on to "Helicon Filter" should have been to "Helicon Focus".

The second one is Focus stacking some issues and remedies. I made this a year ago when I understood a bit more about doing stacking, but my understanding and techniques have developed since then.

So, the videos are out of date, they contain some errors and may not be relevant for your needs. So I mention them very much in the spirit of "For What It Is Worth".
Nick

Flickr
Blog
Journey since 2007

Rework and reposts of my images posted in this forum are always welcome, especially if they come with an explanation of what you did and how you did it.

Post Reply Previous topicNext topic