My Micro Photography Rig

I'd like to get into photomicroscopy.  Specifically, 10X to 20X magnification (but up to 100X) of abstract subjects, printed large on fine art paper and canvas.
  1. Image Gallery page
  2. My current system
  3. My target system
Goals:
  1. I'd like to use this as a learning exercise.  Both in the fundamentals of photomicroscopy.  And in 3D printing to close tolerances and implementing fine control when necessary.
  2. I hope that using high quality components will let me cook up a system capable of high quality images.
  3. I want to be able to make large prints.  Thus, "stack & stitch" capability using the Stackshot rails for X, Y and Z.
  4. I hope to find and adapt older, slightly used, high quality components from eBay, etc.
  5. Speed up my whole image creation process by employing faster hardware and pipelining the process.
 My current system (a work in progress)

Lake Placid, 7 Jun 2019
Here is my current system.  Left to right: a new PC and monitor (for post processing), the old PC and monitor (for capture), the camera.

Regarding the camera (left to right):
(my other objectives and tube lenses are listed here)
  • A cheap but effective X-Y stage mounted on a 3D-printed rotating disc
  • Allowances for a condenser and collimeter
  • A 3D-printed holder for an LED light source
  • The X-Y stage, filters and light source are mounted on an Arca-Swiss rail to a pair of Stackshot rails arranged to move in the X-Y axes (up-down and left-right to support stitching, ie. panoramas)
  • a Stackshot rail in the Z axis (forward and back for focus stacking)
  • A Thorlabs optical breadboard, resting on Sorbothane feet on a fairly solid IKEA dresser on thick carpet on a concrete slab

The X-Y rotating stage makes it easy to move the sample up & down and left & right.  Then to rotate the subject to pose it.
 
The optical breadboard is isolated from my tabletop on the left on which my monitors and keyboards rest.  Still, I leave the room when I'm taking a series of photos (which can be a couple hundred) of say a butterfly wing for focus stacking.
 
At the 42MP resolution of the a7RIII (7952 x 5304px, both with and without Pixel Shift), they should print:
  • 400 dpi at 13" x 20"
     
  • 300 dpi at 18" x 27"
  • 265 dpi at 20" x 30"
(utilizing the full width of my 24" canvas for the width,
  with a 2" border for staples to the frame)
 
(utilizing the full width of my 24" canvas for the height,
  with a 2" border for staples to the frame)

I will update this section periodically as I develop the system.
References:
   - 52MM STUDIO SETUP (after which I modelled my setup)
   - Matching Camera to Microscope Resolution
which I've plotted here -->
The dotted horizontal line (at Pixel Size = 4.5 µm) corresponds to my a7RIII (not counting the presumed benefits of Pixel Shift).  My Mitutoyo objectives are marked.
 
The Mitutoyos have a decreasing cost-performance benefit to resolution at higher magnifications.  It is possible that the benefits of these objectives at the higher magnifications are increased Working Distance and reduced Chromatic Aberation (due to them being APO).
 
I think this plot shows that my a7RIII is capable of out-resolving my Mitutoyo objectives (but not by
much for the 10X.. not counting the benefit of Pixel Shift). 
 
Note, this plot is based on traditional microscope design (the text refers to aligning the condenser and matching the condenser's NA to the objective's NA), so I may be mixing apples and oranges.
Camera
Lake Placid, 13 Jul 2019
I have a Sony a7RIII.  Here is a look at the a7RIII image quality from Digital Camera Review's website compared with the Pentax K-1 Mark II (which also has pixel shift) and Canon and Nikon cameras.
 
Click on the image to enlarge it or on the link above to use the tool.
 
Here is a look at the a7RIII dynamic range from the Photons to Photos website.  It is the black line.  The Phase One IQ4 (blue line) bests it but that is a medium format $52,000 camera.  The Pentax K-1 Mark II beats it but at higher ISOs.  I am able to control the lighting and exposure and am shooting at the lowest ISO (where many of the cameras converge in any case - about 11½ stops).
 
DXOMARK has ranked the a7RIII favorably since the camera came out.
 
Pixel shift appears to have some benefit to resolution -- although it is reported that Sony's post processing tool, Imaging Edge, sharpens the result when it creates the combined image.  But when I've just eyeballed it at 100%, I think I've seen detail in the combined image that is not simply the result of sharpening (it could be I'm looking at it wrong).  In any case, I will look at using other tools (e.g. SonyPixelShift2DNG, Raw Therapee) as noted in that article.
 
There do appear to be benefits using pixel shift of reduced moiré, reduced noise and improved color accuracy.
 
I realize this all has very little, if any, effect at "web page image sizes".  My hope is that its benefits will come into play at large format print sizes.

Polarizer
Armenia, 7 Apr 2019                 Tests
I want to make polarized photos like the crystals on my gallery page.  It looks like that calls for 2 polarizing filters, a "retardation or wave plate" (mica, scotch tape or I'm going to try this retarder film) and a holder for the microscope slide. 
 
I'm planning to 3D-print a holder for them.  Click on the animation ->
One polarizer (called the Analyzer) and the Retardation Plate would be located in the tube between the tube lens and the objective.  The Slide and other
Glass polarizers
Retarder film
A 3D-printed holder
with condenser
Polarizer would be held in the 3D-printed holder.  The light panel in this animation is an LED light source such as this one.
Printer
Lake Placid, 13 Jul 2019
Here is the printer I'm using - a Canon Pro-4000.  It is capable of printing on 44" wide media.  I expect to mainly make 20" x 30" prints on canvas and fine art paper.  But have the ability to print much larger.
A fast PC (PC2)
Armenia, 5 Apr 2019
This will run Zerene doing the image stacking (using Zerene's "capability to ingest and stack new images on the fly as they are acquired by a tethered camera").  PC2 also runs Photoshop and Zerene for post processing. 
 
I expect to use an Intel i9-9900K (8 cores, 5 GHz), 64 GB RAM, 1 TB SSD, Windows 10, a good calibrated 4K monitor.
 My Target system

Armenia, 25 Apr 2019
Lake Placid, 7 Jun 2019
Optically, this is the sort of system (left) I'd like to initally emulate using my components (right).  That is, add to my current system the linear polarizers, retardation
material, a light source and whatever bits of 3D-printed holders I need to glue it all together (the grey and yellow parts in the animation).

This is the process I will use to develop the rig for photographing crystals:

I feel it takes a long time to process a large stack - converting the Raw Pixel Shift images from the camera to TIFFs for Zerene being much of it.  It requires several manual steps - easy drag-and-drop operations, but I have to be there to do it.  I'd like to speed up the process by souping up my computer system and removing the manual steps.
 
Computationally, this is the system I'd like to build.  My goal is to automate the end-to-end process.  And convert and stack the images as they come off the camera.  To accomplish that, I am putting together a Multi-processor (MP) from single board computers (Raspberry Pi's)
and planning to build a fast PC (PC2) to do the stacking and post processing.
 
I'm planning to locate the MP, NAS and Ethernet switch in a separate room to avoid their cooling fans from affecting the image capture.  Everything is connected together by Gigabit Ethernet.  There is also a Wifi connection from the Controller on PC1 to a web server-based monitor so I can check on status using my laptop, tablet or phone.
 
Status: My new MP monitor based on my old Raspi Monitor is coming along.
 
References:
- Old Microscopes
Leitz Dialux, Early 1970s many parts and accessories are available on the market
American Optical Series 110, Mid-1980s [a so-so review]
Zeiss Standard, Late 1970s higher level are the Universal or Photomic models
Nikon Labophot, Mid-1980s an "entry level" benchtop scope, less expensive than the Optiphot line (which are rare in POL), unsurpassed optics, large controls
Wild Heerbrugg M21, Early 1970s considered by some experts to be the best microscope ever made
Olympus BH-2 BHTP, Late 1980s "the microscope I prefer over all others"
- New Microscopes
- Research Microscopes
Mesolens:
Mesolab website -- 4X mag, NA 0.47, field size 6mm, WD 3mm, resolution 0.7 µm lateral, 7 µm axial
In which they claim, "For more than 100 years, the ratio of magnification to NA has been held at approximately 40:1 for all microscope objectives."  I've plotted Magnification vs NA for the objectives I'm interested in (infinity focus, non-oil).  ...
 
 
 
 
 
 
 
 
 
Polychromatic polarization microscope:
- DIY Microscopes
        Bertrand Filters
            New Bertrand Lens on Ebay
        Condensers
            Substage Condensers
        Lighting
            Tungsten halogen vs white LED
            Optiphot modular light source
            FAQ:How (and why) to use electronic flash at the microscope?
            Microscope Conversion to LED-Light
            HOW BRIGHT IS YOUR LIGHT PART III: LED CONVERSION
        Rheinberg Filters
            Making Rheinberg illumination discs
            How to Make Rheinberg Filters
            Rheinberg Filters for Photomicrography
   - Technique
            A Practical Guide to Creating Superresolution Photos with Photoshop
Raspberry Pi MP
Armenia, 15 Apr 2019                 Implementation
I'd like to build this Multiprocessor out of the latest version of the Raspberry Pi (Raspberry Pi 3 Model B+).  The Pi 3 B+ is clocked at 1.4 GHz, has 1 TB of RAM and supports Gigabit Ethernet at 300 Mbps.
 
I will model mine after Joshua Kiepert's RPiCluster.  He has documented his system well, including Eagle files for his power distribution cards.
 
At the end of that article, it says his 32-node system (using an older version of Raspberry Pi) does 10.13 GFlops, where "the first Cray-2 supercomputer in 1985
did 1.9 GFlops".  I look forward to benchmarking mine.  Let's see, Summit did 200,795 TFlops in the latest Nov 2018 Top500 List.  How close will I be?
Ethernet Switch
Armenia, 12 Apr 2019
I'd like to be able to support up to 48 Raspberry Pi's.  Add a port for the Master Node, two for the NAS, one for the PC1+PC2 (that I'll bring in from a separate switch where they're located at
my desk).  Making 52 ports all together.  This 52 port switch looks good.  Gigabit speed at a reasonable price.
Network Attached Server (NAS)
Armenia, 25 Apr 2019
This one looks good.  Five bays plus an optional 5-bay add-on.  140 TB (70 TB + 14 TB drive x 5) capacity.  Two Ethernet ports.  Good reviews.  At a reasonable price.
FIN