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Leica S4E & S8APO

<r><l>
Author:{{{author}}}
Updated:{{{modification-time(%Y-%m-%d)}}}

Copyright {{{time(%Y)}}} Mitch Richling. All rights reserved.

Check out my home page for more stuff: https://www.mitchr.me/

1 Introduction

This page contains my personal notes for the Leica S8APO & S4E stereo microscopes. Being my personal notes, the content here isn’t terribly polished; however, I’ve gone ahead and published it anyhow in hope someone might find it useful.

2 Microscope Symbols & Formulas

2.1 Variables

Variable Description Units Notes
$S_{MAG}$ Magnification At Sensor Ratio
$S_{FOVh}$ Sensor Horizontal Field Of View mm
$S_{FOVv}$ Sensor Vertical Field Of View mm
$I_{SCLh}$ Image Horizontal Scale Pixel/mm
$I_{SCLv}$ Image Vertical Scale Pixel/mm
$S_w$ Sensor Physical Width mm
$S_h$ Sensor Physical Height mm
$S_d$ Sensor Physical Diagonal mm
$S_A$ Sensor Physical Area square mm
$I_w$ Image/Sensor Pixel Width pixel
$I_h$ Image/Sensor Pixel Height pixel
$I_{MP}$ Total number of Image/Sensor Pixels Megapixel
$L_s$ Length At Sensor mm
$L_o$ Object Length mm
$A$ Auxiliary Ratio
$Z$ Zoom Ratio
$O_c$ Camera Objective Ratio camera relay lens, camera port lens
$O_d$ Camera Objective Image Circle Diameter mm
$P_w$ Sensor Pixel Width mm
$P_h$ Sensor Pixel Height mm
$P_{AR}$ Pixel Aspect Ratio Ratio
$V_{FOV}$ Visual Field Of View mm
$E_{FN}$ Eyepiece Field Number mm
$E_{MAG}$ Eyepiece magnification Ratio
$V_{MAG}$ Visual Magnification Ratio
$R_c$ Reticle Unit Conversion Factor mm/Ru $1\,\mathrm{Ru}=1\,\mathrm{mmu}$ @ $Z=1$ & $A=1$
$R_s$ Reticle Scale mm/Ru
$L_R$ Length in Reticle Units Ru
$I_{AR}$ Image Aspect Ratio Ratio
$P_{IJSPAR}$ ImageJ Scale Pixel Aspect Ratio Ratio
$W$ Working Distance mm

2.2 Formulas

Image/Sensor magnification
$$S_{MAG} = \frac{L_s}{L_o} = A ⋅ Z ⋅ O_c$$
Image/Sensor Horizontal Field Of View
$$S_{FOVh} = \frac{min(O_d, S_w)}{S_{MAG}}$$
Image/Sensor Vertical Field Of View
$$S_{FOVv} = \frac{min(O_d, S_h)}{S_{MAG}}$$
Image/Sensor Horizontal Scale
$$I_{SCLh} = \frac{S_{MAG} ⋅ I_w}{S_w} = \frac{S_{MAG}}{P_w}$$
Image/Sensor Vertical Scale
$$I_{SCLv} = \frac{S_{MAG} ⋅ I_h}{S_h} = \frac{S_{MAG}}{P_h}$$
Visual magnification
$$V_{MAG} = A ⋅ Z ⋅ E_{MAG}$$
Visual Field Of View
$$V_{FOV} = \frac{E_{FN}}{A ⋅ Z}$$
Reticle Scale
$$\frac{R_c}{Z ⋅ A}$$
Reticle Length Measurements
$$\mathrm{Length}=R_s ⋅ L_R$$
Sensor Diagonal length
$$S_d = \sqrt{S_w^2 + S_h^2}$$
Sensor Pixel Width
$$P_w = \frac{S_w}{I_w}$$
Sensor Pixel Height
$$P_h = \frac{S_h}{I_h}$$
Pixel Aspect Ratio
$$P_{AR} = \frac{P_w}{P_h} = \frac{S_w ⋅ I_h}{I_w ⋅ S_h}$$
Image Aspect Ratio
$$I_{AR} = \frac{I_w}{I_h}$$
ImageJ Scale Pixel Aspect Ratio
$$P_{IJSPAR} = \frac{1}{P_{AR}}$$

3 Local Documentation

  • /Users/richmit/Documents/Doc2/gadgets/leica_microscopes/cameras
  • /Users/richmit/Documents/Doc2/gadgets/leica_microscopes/S4-S6-S8APO
  • /Users/richmit/Documents/Doc2/gadgets/leica_microscopes/S8APO
  • /Users/richmit/Documents/Doc2/gadgets/leica_microscopes/S9-S8APO
  • /Users/richmit/Documents/Doc2/gadgets/leica_microscopes/whitepapers

4 S4E

4.1 Magnification and FOV at Various Zoom Levels With 10x/23 Eyepiece

$A=$ $W=$ $A=$ $W=$ $A=$ $W=$ $A=$ $W=$ $A=$ $W=$
$0.5×$ $200\,\mathrm{mm}$ $0.75×$ $130\,\mathrm{mm}$ $1.0×$ $110\,\mathrm{mm}$ $1.6×$ $55\,\mathrm{mm}$ $2.0×$ $35\,\mathrm{mm}$
$Z$ $E_{MAG}$ $V_{FOV}$ $E_{MAG}$ $V_{FOV}$ $E_{MAG}$ $V_{FOV}$ $E_{MAG}$ $V_{FOV}$ $E_{MAG}$ $V_{FOV}$
/ 23 10
^ EFN EMAG
/ 0.5 0.75 1 1.6 2.0
/ < > < > < > < > < >
0.63 3.15 73.02 4.72 48.68 6.30 36.51 10.08 22.82 12.60 18.25
0.80 4.00 57.50 6.00 38.33 8.00 28.75 12.80 17.97 16.00 14.38
1.00 5.00 46.00 7.50 30.67 10.00 23.00 16.00 14.38 20.00 11.50
1.25 6.25 36.80 9.38 24.53 12.50 18.40 20.00 11.50 25.00 9.20
1.60 8.00 28.75 12.00 19.17 16.00 14.38 25.60 8.98 32.00 7.19
2.00 10.00 23.00 15.00 15.33 20.00 11.50 32.00 7.19 40.00 5.75
2.50 12.50 18.40 18.75 12.27 25.00 9.20 40.00 5.75 50.00 4.60
3.00 15.00 15.33 22.50 10.22 30.00 7.67 48.00 4.79 60.00 3.83

4.2 Reticle Scale, Magnification, and FOV at Zoom Stops With 10x/23 Eyepiece

$A$ $Z$ $E_{MAG}$ $E_{FN}$ $R_s$ $V_{MAG}$ $V_{FOV}$
/ < >
0.50 0.63 10 23 3.17460 3.15 73.02
0.50 3.00 10 23 0.66667 15.00 15.33
0.75 0.63 10 23 2.11640 4.72 48.68
0.75 3.00 10 23 0.44444 22.50 10.22
1.00 0.63 10 23 1.58730 6.30 36.51
1.00 3.00 10 23 0.33333 30.00 7.67
1.60 0.63 10 23 0.99206 10.08 22.82
1.60 3.00 10 23 0.20833 48.00 4.79
2.00 0.63 10 23 0.79365 12.60 18.25
2.00 3.00 10 23 0.16667 60.00 3.83

5 S8APO

5.1 Magnification and FOV at Various Zoom Levels With 10x/23 Eyepiece

$A=$ $W=$ $A=$ $W=$ $A=$ $W=$ $A=$ $W=$
$0.32×$ $200\,\mathrm{mm}$ $0.63×$ $101\,\mathrm{mm}$ $1.0×$ $75\,\mathrm{mm}$ $2.0×$ $25\,\mathrm{mm}$
$Z$ $V_{MAG}$ $V_{FOV}$ $V_{MAG}$ $V_{FOV}$ $V_{MAG}$ $V_{FOV}$ $V_{MAG}$ $V_{FOV}$
/ 23 10
^ EFN EMAG
/ 0.32 0.63 1.0 2.0
/ < > < > < > < >
1.0 3.2 71.88 6.30 36.51 10.0 23.00 20 11.50
1.25 4.0 57.50 7.88 29.21 12.5 18.40 25 9.20
1.6 5.1 44.92 10.08 22.82 16.0 14.38 32 7.19
2.0 6.4 35.94 12.60 18.25 20.0 11.50 40 5.75
2.5 8.0 28.75 15.75 14.60 25.0 9.20 50 4.60
3.2 10.2 22.46 20.16 11.41 32.0 7.19 64 3.59
4.0 12.8 17.97 25.20 9.13 40.0 5.75 80 2.88
5.0 16.0 14.38 31.50 7.30 50.0 4.60 100 2.30
6.3 20.2 11.41 39.69 5.79 63.0 3.65 126 1.83
8.0 25.6 8.98 50.40 4.56 80.0 2.88 160 1.44

5.2 Reticle Scale, Magnification, and FOV at Zoom Stops With 10x/23 Eyepiece

$A$ $Z$ $E_{MAG}$ $E_{FN}$ $R_s$ $V_{MAG}$ $V_{FOV}$
/ < >
0.32 1 10 23 3.12500 3.20 71.88
0.32 8 10 23 0.39062 25.60 8.98
0.63 1 10 23 1.58730 6.30 36.51
0.63 8 10 23 0.19841 50.40 4.56
1.00 1 10 23 1.00000 10.00 23.00
1.00 8 10 23 0.12500 80.00 2.88
2.00 1 10 23 0.50000 20.00 11.50
2.00 8 10 23 0.06250 160.00 1.44

5.3 Numerical Aperture With No Auxiliary Lens

ZoomNA
1.00.026
1.250.031
1.60.038
2.00.046
2.50.056
3.20.069
4.00.081
5.00.093
6.30.100
8.00.100

5.4 Leica C-Mount Video Objective Data

Leica Part # Leica Part Name Mag $O_d$ Notes Ref
<r> <l> <r> <l> <c>
/ <>
10445928 Leica Video Objective $0.32×$ 0.32 6.7 Estimated $O_d$ co32
10450528 Leica Video Objective $0.5×$ 0.50 10.5 Measured $O_d$ co50
10447367 Leica Video Objective $0.63×$ 0.63 13.2 Estimated $O_d$ co63
10446307 Leica Video Objective $0.8×$ 0.80 16.8 Estimated $O_d$ co80

Note the image circles are all the same size at the sensor for a particular video objective, but FOV will change with the auxiliary & video objective.

With $O_d=0.5×$ we can capture the full image circle with a Micro Four Thirds (Olympus OM-D E-M1 Mark II) sensor, but only about 37% of the image circle with an IMX477 (RPI HQ) sensor. Note that about 65% of the Micro Four Thirds sensor is outside the image circle – i.e. wasted pixels.

$Z=1$ $Z=8$
$A=0.63$ 10450528-10446335-z1_200.png 10450528-10446335-z8_200.png
$A=1.00$ 10450528-NONE-z1_200.png 10450528-NONE-z8_200.png

With $O_d=0.32×$ the image circle shrinks, and now we can capture about 76% of the image circle with an IMX477 (RPI HQ); however, about 3% percent of the sensor is outside the image circle – i.e. wasted sensor pixels. Note that with the smaller image circle the Micro Four Thirds sensor is even less efficiently used with about 84% of the sensor pixels wasted.

$Z=1$ $Z=8$
$A=0.63$ 10445928-10446335-z1_200.png 10445928-10446335-z8_200.png
$A=1.00$ 10445928-NONE-z1_200.png 10445928-NONE-z8_200.png

5.4.1 Annotating Image Circle Images

rm *.png

echo anno 10450528-10446335-z1.jpg
convert 10450528-10446335-z1.jpg -rotate 180 -pointsize 100 -draw "gravity northwest fill white text 10,10 'Z=1  A=0.63x  C=0.50x'" -draw "gravity northwest fill red text 4300,1944 '32 mm'"  -draw "gravity southeast fill blue text 1700,1239 'RPI HQ'" -draw "gravity southwest fill green text 4350,10 'Micro Four Thirds'" -fill none -stroke red -strokewidth 10 -draw 'circle 2592,1944 4093,1944' -stroke blue -draw 'rectangle 1655,1239 3529,2649' -stroke green -draw 'rectangle 1,1 5184,3888' 10450528-10446335-z1.png; 
echo anno 10450528-10446335-z8.jpg
convert 10450528-10446335-z8.jpg -rotate 180 -pointsize 100 -draw "gravity northwest fill white text 10,10 'Z=8  A=0.63x  C=0.50x'" -draw "gravity northwest fill red text 4300,1944 '4 mm'"   -draw "gravity southeast fill blue text 1700,1239 'RPI HQ'" -draw "gravity southwest fill green text 4350,10 'Micro Four Thirds'" -fill none -stroke red -strokewidth 10 -draw 'circle 2592,1944 4093,1944' -stroke blue -draw 'rectangle 1655,1239 3529,2649' -stroke green -draw 'rectangle 1,1 5184,3888' 10450528-10446335-z8.png; 
echo anno 10450528-NONE-z1.jpg  
convert 10450528-NONE-z1.jpg     -rotate 180 -pointsize 100 -draw "gravity northwest fill white text 10,10 'Z=1  A=1.00x  C=0.50x'" -draw "gravity northwest fill red text 4300,1944 '20 mm'"  -draw "gravity southeast fill blue text 1700,1239 'RPI HQ'" -draw "gravity southwest fill green text 4350,10 'Micro Four Thirds'" -fill none -stroke red -strokewidth 10 -draw 'circle 2592,1944 4093,1944' -stroke blue -draw 'rectangle 1655,1239 3529,2649' -stroke green -draw 'rectangle 1,1 5184,3888' 10450528-NONE-z1.png; 
echo anno 10450528-NONE-z8.jpg
convert 10450528-NONE-z8.jpg     -rotate 180 -pointsize 100 -draw "gravity northwest fill white text 10,10 'Z=8  A=1.00x  C=0.50x'" -draw "gravity northwest fill red text 4300,1944 '2.5 mm'" -draw "gravity southeast fill blue text 1700,1239 'RPI HQ'" -draw "gravity southwest fill green text 4350,10 'Micro Four Thirds'" -fill none -stroke red -strokewidth 10 -draw 'circle 2592,1944 4093,1944' -stroke blue -draw 'rectangle 1655,1239 3529,2649' -stroke green -draw 'rectangle 1,1 5184,3888' 10450528-NONE-z8.png; 

echo anno 10445928-10446335-z1.jpg
convert 10445928-10446335-z1.jpg -rotate 180 -pointsize 100 -draw "gravity northwest fill white text 10,10 'Z=1  A=0.63x  C=0.32x'" -draw "gravity northwest fill red text 3800,1944 '34 mm'"  -draw "gravity southeast fill blue text 1700,1239 'RPI HQ'" -draw "gravity southwest fill green text 4350,10 'Micro Four Thirds'" -fill none -stroke red -strokewidth 10 -draw 'circle 2592,1944 3617,1944' -stroke blue -draw 'rectangle 1655,1239 3529,2649' -stroke green -draw 'rectangle 1,1 5184,3888' 10445928-10446335-z1.png;
echo anno 10445928-10446335-z8.jpg
convert 10445928-10446335-z8.jpg -rotate 180 -pointsize 100 -draw "gravity northwest fill white text 10,10 'Z=8  A=0.63x  C=0.32x'" -draw "gravity northwest fill red text 3800,1944 '4.3 mm'" -draw "gravity southeast fill blue text 1700,1239 'RPI HQ'" -draw "gravity southwest fill green text 4350,10 'Micro Four Thirds'" -fill none -stroke red -strokewidth 10 -draw 'circle 2592,1944 3617,1944' -stroke blue -draw 'rectangle 1655,1239 3529,2649' -stroke green -draw 'rectangle 1,1 5184,3888' 10445928-10446335-z8.png; 
echo anno 10445928-NONE-z1.jpg  
convert 10445928-NONE-z1.jpg     -rotate 180 -pointsize 100 -draw "gravity northwest fill white text 10,10 'Z=1  A=1.00x  C=0.32x'" -draw "gravity northwest fill red text 3800,1944 '21 mm'"  -draw "gravity southeast fill blue text 1700,1239 'RPI HQ'" -draw "gravity southwest fill green text 4350,10 'Micro Four Thirds'" -fill none -stroke red -strokewidth 10 -draw 'circle 2592,1944 3617,1944' -stroke blue -draw 'rectangle 1655,1239 3529,2649' -stroke green -draw 'rectangle 1,1 5184,3888' 10445928-NONE-z1.png; 
echo anno 10445928-NONE-z8.jpg
convert 10445928-NONE-z8.jpg     -rotate 180 -pointsize 100 -draw "gravity northwest fill white text 10,10 'Z=8  A=1.00x  C=0.32x'" -draw "gravity northwest fill red text 3800,1944 '2.7 mm'" -draw "gravity southeast fill blue text 1700,1239 'RPI HQ'" -draw "gravity southwest fill green text 4350,10 'Micro Four Thirds'" -fill none -stroke red -strokewidth 10 -draw 'circle 2592,1944 3617,1944' -stroke blue -draw 'rectangle 1655,1239 3529,2649' -stroke green -draw 'rectangle 1,1 5184,3888' 10445928-NONE-z8.png; 

for f in *.png; do
  for s in 200 800; do
    echo $f $s
    nn=`echo $f | sed "s/.png\$/_$s.png/"`
    convert $f -resize x$s $nn
  done
done

cp *_*.png ~/world/my_prog/microscope/docs

echo DONE

5.5 Attaching Cameras

The Leica documentation suggests using a chain of adapters for attaching a generic digital camera. The first part of the chain is one of the following three parts: 10447436 1.6× DSLR tube, 10446175 2.5× DSLR tube, or 10445930 1.0× video/photo objective. Next will be one or more adapters for your camera. The result can be a tower of adapters taller than your microscope! For cameras with large sensors, this really is the only way to go. An excellent write-up for this approach may be found here. A good discussion on MicrobeHunter.com may found here.

For cameras with Micro Four Thirds and smaller sensors, a simpler approach is connect your camera via a c-mount adapter to one of Leica’s “C-Mount Video Objectives”: 10445928 $0.32×$, 10450528 $0.5×$, 10447367 $0.63×$, or 10446307 $0.8×$. These adapters are intended to be used with Leica’s microscope cameras, but they will work with any c-mount camera – including your SLR with a c-mount adapter.

With the $0.5×$ objective one will obtain a nice 10.5mm image circle which is just about perfect for whole field imaging with the 13mm tall sensor in a Micro Four Thirds camera.

I use two cameras with my S8APO:

5.6 Camera FOV & Image Scales

RPI OLY
$A$ $Z$ $O_c$ $O_d$ $S_{MAG}$ $P_{IJSPAR}$ $I_{SCLh}$ $I_{SCLv}$ $S_{FOVh}$ $S_{FOVv}$ $P_{IJSPAR}$ $I_{SCLh}$ $I_{SCLv}$ $S_{FOVh}$ $S_{FOVv}$
! A Z Oc Od SMAG RPI_PIJSPAR RPI_ISCLH RPI_ISCLV RPI_SFOVH RPI_SFOVV OLY_PIJSPAR OLY_ISCLH OLY_ISCLV OLY_SFOVH OLY_SFOVV
/ 6.2868 4.712 4056 3040 17.4 13 5184 3888
^ RPI_Sw RPI_Sh RPI_Iw RPI_Ih OLY_Sw OLY_Sh OLY_Iw OLY_Ih
/ < > < >
0.63 1 0.50 10.5 0.32 1.0000000 203.23 203.23 19.96 14.96 0.9961686 93.85 94.21 33.33 33.33
0.63 8 0.50 10.5 2.52 1.0000000 1625.81 1625.81 2.49 1.87 0.9961686 750.79 753.67 4.17 4.17
1.00 1 0.50 10.5 0.50 1.0000000 322.58 322.58 12.57 9.42 0.9961686 148.97 149.54 21.00 21.00
1.00 8 0.50 10.5 4.00 1.0000000 2580.65 2580.65 1.57 1.18 0.9961686 1191.72 1196.31 2.62 2.62
2.00 1 0.50 10.5 1.00 1.0000000 645.16 645.16 6.29 4.71 0.9961686 297.93 299.08 10.50 10.50
2.00 8 0.50 10.5 8.00 1.0000000 5161.29 5161.29 0.79 0.59 0.9961686 2383.45 2392.62 1.31 1.31

6 S4 and S8 Magnification Coverage

Various magnifications may be reached with different combinations of eyepiece, power, & auxiliary lens.

  • green: Full APO
  • yellow: Achro but not APO
  • pink: Unspecified distortion (might not even be Acro)
  • red: I don’t have equipment for this
  • black: Not possible
S/EPxA{{{SPP(003)}}}{{{SPP(004)}}}{{{SPP(005)}}}{{{SPP(006)}}}{{{SPP(008)}}}{{{SPP(010)}}}{{{SPP(013)}}}{{{SPP(016)}}}{{{SPP(020)}}}{{{SPP(026)}}}{{{SPP(032)}}}{{{SPP(040)}}}{{{SPP(050)}}}{{{SPP(064)}}}{{{SPP(080)}}}{{{SPP(100)}}}{{{SPP(128)}}}{{{SPP(160)}}}{{{SPP(200)}}}{{{SPP(256)}}}{{{SPP(320)}}}{{{SPP(400)}}}{{{SPP(500)}}}{{{SPP(640)}}}
/<c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c><c>
{{{SPP(S4/10x0.50)}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/10x0.32)}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/10x0.75)}}}{{{XBX}}}{{{XBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/16x0.50)}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/10x1.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/10x0.63)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/10x0.75)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/25x0.50)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/10x1.60)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/10x1.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{ABX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/20x1.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/10x2.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{CBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/20x0.63)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/16x1.60)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/16x1.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/20x1.60)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/10x2.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{UBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/25x1.60)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/25x1.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/16x2.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S4/40x1.60)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/40x1.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/25x2.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{XBX}}}{{{XBX}}}
{{{SPP(S8/40x2.00)}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{XBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}{{{MBX}}}

7 Reticle Unit Conversion Software For free42 and DM42

The computational part of this code is trivial. The value of the program really is in the settings menus – allowing the user to quickly change equipment settings and convert measurements.

The code as-is will work pretty well for people using an S8APO or S4E scope with a 10x EP and standard reticle; however, users with diffrent equipment will want to modify the settings menus.

7.1 The menu

KeyWithout [SHIFT]With [SHIFT]Notes
/<>
AStore ADisplay AStored in variable “mrcvA”
ZStore ZDisplay ZStored in variable “mrcvZ”
RcStore RcDisplay RcStored in variable “mrcvRc”
▒▒▒▒
▒▒▒▒
CONVConvert from Reticle UnitsConvert from Reticle Units
8;.32Leica S8APO; Z=1.00x; A=0.32x auxLeica S8APO; Z=8.00x; A=0.32x aux
8;.63Leica S8APO; Z=1.00x; A=0.63x auxLeica S8APO; Z=8.00x; A=0.63x aux
8;1Leica S8APO; Z=1.00x; A=1.00x (no aux)Leica S8APO; Z=8.00x; A=1.00x (no aux)
8;1.6Leica S8APO; Z=1.00x; A=1.60x auxLeica S8APO; Z=8.00x; A=1.60x aux
8;2Leica S8APO; Z=1.00x; A=2.00x auxLeica S8APO; Z=8.00x; A=2.00x aux
ZZZLeica S8APO; Z=1.00x; A=NO CHANGELeica S8APO; Z=8.00x; A=NO CHANGE
4;.32Leica S4; Z=0.63x; A=0.32x auxLeica S4; Z=3.00x; A=0.32x aux
4;.5Leica S4; Z=0.63x; A=0.50x auxLeica S4; Z=3.00x; A=0.50x aux
4;.63Leica S4; Z=0.63x; A=0.63x auxLeica S4; Z=3.00x; A=0.63x aux
4;.75Leica S4; Z=0.63x; A=0.75x auxLeica S4; Z=3.00x; A=0.75x aux
4;1Leica S4; Z=0.63x; A=1.00x (no aux)Leica S4; Z=3.00x; A=1.00x (no aux)
4;1.6Leica S4; Z=0.63x; A=1.60x auxLeica S4; Z=3.00x; A=1.60x aux

7.2 The code

The code below may be cut-n-pasted the code below into free42. Alternately the raw file from github.

@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ (ref:MRCONV)
@@@@ DSC: Convert Reticle Units to Physical Units
LBL "MRCONV"

LBL 01           @@@@ Conversion & Variable Menu Page
CLMENU
"A"
KEY 1 XEQ 11
"Z"
KEY 2 XEQ 12
"Rc"
KEY 3 XEQ 13
"CONV"
KEY 6 XEQ 14
KEY 7 GTO 03
KEY 8 GTO 02
KEY 9 GTO 00
MENU
STOP
GTO 01

LBL 02           @@@@ Quick Settings Menu Page #1
CLMENU
"8;.32"            @@@@ Setting: S8 with 0.32x aux
KEY 1 GTO 20       
"8;.63"            @@@@ Setting: S8 with 0.63x aux
KEY 2 GTO 21       
"8;1"              @@@@ Setting: S8 with no aux
KEY 3 GTO 22       
"8;1.6"            @@@@ Setting: S8 with 1.6x aux
KEY 4 GTO 23       
"8;2"              @@@@ Setting: S8 with 2x aux
KEY 5 GTO 24       
"ZZZ"              @@@@ Setting: Toggle Zoom
KEY 6 XEQ 25
KEY 7 GTO 01
KEY 8 GTO 03
KEY 9 GTO 00
MENU
STOP
GTO 02

LBL 03           @@@@ Quick Settings Menu Page #2
CLMENU
"4;.32"            @@@@ Setting: S4 with 0.32x aux
KEY 1 GTO 30       
"4;.5"             @@@@ Setting: S4 with 0.5x aux
KEY 2 GTO 31       
"4;.63"            @@@@ Setting: S4 with 0.63x aux
KEY 3 GTO 32       
"4;.75"            @@@@ Setting: S4 with 0.75x aux
KEY 4 GTO 33       
"4;1"              @@@@ Setting: S4 with no aux
KEY 5 GTO 34       
"4;1.6"            @@@@ Setting: S4 with 1.6x aux
KEY 6 XEQ 35
KEY 7 GTO 02
KEY 8 GTO 01
KEY 9 GTO 00
MENU
STOP
GTO 03

LBL 00           @@@@ Application Exit
EXITALL          
RTN              

LBL 11           @@@@ Code for menu key A
FC? 64           
STO "mrcvA"      
VIEW "mrcvA"     
RTN              
LBL 12           @@@@ Code for menu key Z
FC? 64           
STO "mrcvZ"      
VIEW "mrcvZ"     
RTN              
LBL 13           @@@@ Code for menu key Rc
FC? 64           
STO "mrcvRc"     
VIEW "mrcvRc"    
RTN              
LBL 14           @@@@ Code for menu key CONV
RCL× "mrcvRc"    
RCL÷ "mrcvA"     
RCL÷ "mrcvZ"     
RTN              

LBL 20           @@@@ Code for Setting S8: with 0.32x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
0.32               @@@@ A Value
STO "mrcvA"      
GTO 26             @@@@ Set Z Value
LBL 21           @@@@ Code for Setting: S8 with 0.63x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
0.63               @@@@ A Value
STO "mrcvA"      
GTO 26             @@@@ Set Z Value
LBL 22           @@@@ Code for Setting: S8 with no aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
1.00               @@@@ A Value
STO "mrcvA"      
GTO 26             @@@@ Set Z Value
LBL 23           @@@@ Code for Setting: S8 with 1.6x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
1.60               @@@@ A Value
STO "mrcvA"      
GTO 26             @@@@ Set Z Value
LBL 24           @@@@ Code for Setting: S8 with 2x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
2.00               @@@@ A Value
STO "mrcvA"      
GTO 26             @@@@ Set Z Value
LBL 25           @@@@ Code for Setting: EMPTY
GTO 26             @@@@ Set Z Value

LBL 26 @@@@ Drop X & set the zoom level for S8 Scope
R↓               
FC? 64           
1.0               @@@@ Z Value NO SHIFT
FS? 64           
8.0               @@@@ Z Value SHIFT
STO "mrcvZ"      
GTO 01

LBL 30           @@@@ Code for Setting: S4 with 0.32x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
0.32               @@@@ A Value
STO "mrcvA"      
GTO 36             @@@@ Set Z Value
LBL 31           @@@@ Code for Setting: S4 with 0.5x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
0.50               @@@@ A Value
STO "mrcvA"      
GTO 36             @@@@ Set Z Value
LBL 32           @@@@ Code for Setting: S4 with 0.63x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
0.63               @@@@ A Value
STO "mrcvA"      
GTO 36             @@@@ Set Z Value
LBL 33           @@@@ Code for Setting: S4 with 0.75x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
0.75               @@@@ A Value
STO "mrcvA"      
GTO 36             @@@@ Set Z Value
LBL 34           @@@@ Code for Setting: S4 with no aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
1.00               @@@@ A Value
STO "mrcvA"      
GTO 36             @@@@ Set Z Value
LBL 35           @@@@ Code for Setting: S4 with 1.6x aux
1                  @@@@ Rc Value
STO "mrcvRc"     
R↓               
1.60               @@@@ A Value
STO "mrcvA"      
GTO 36             @@@@ Set Z Value

LBL 36 @@@@ Drop X & Set the zoom level for S4 Scope
R↓               
FC? 64           
0.63               @@@@ Z Value NO SHIFT
FS? 64           
3.0                @@@@ Z Value SHIFT
STO "mrcvZ"      
GTO 01

END

8 S-Series Leica Parts

Leica Part # Leica Part Name
< < >
1 10446298 Leica S8 APO
1 10446293 Leica S4 E
2 10447136 10x/23B eyepiece for eyeglasses, fixed
4 10447137 10x/23B eyepiece for eyeglasses, adjustable
10447138 16x/15B eyepiece for eyeglasses, fixed
10447139 16x/15B eyepiece for eyeglasses, adjustable
10446447 Reticle 10 mm/0.1 mm
10446448 Reticle 5 mm/0.1 mm
10446449 Reticle 5 mm/0.05 mm
10447000 Reticle 100 scale intervals / 0.002”
10447001 Reticle 100 scale intervals / 0.001”
10447002 Reticle 150 scale intervals / 0.0005”
1 10446334 Achro Auxiliary $0.32×$ for S8APO, WD 200 mm
1 10446335 APO Auxiliary $0.63×$ for S8APO, WD 100 mm
10446336 APO Auxiliary $1.6×$ for S8APO, WD 37 mm
10446337 APO Auxiliary $2.0×$ for S8APO, WD 25 mm
10446316 Auxiliary $0.32×$ for S4/S6, WD 300 mm
1 10446318 Auxiliary $0.5×$ for S4/S6, WD 200 mm
10446319 Auxiliary $0.63×$ for S4/S6, WD 155 mm
1 10446320 Auxiliary $0.75×$ for S4/S6, WD 130 mm
1 10446321 Auxiliary $1.6×$ for S4/S6, WD 55 mm
1 10446322 Auxiliary $2.0×$ for S4/S6, WD 35 mm
10446325 Auxiliary $0.3–0.4×$ for S4/S6 (Adjustable), WD 200–350mm
10446323 Auxiliary $0.6–0.75×$ for S4/S6 (ErgoObjective) WD 77–137mm
10446324 Lens shield
10450831 Updated lens shield
1 10445928 Leica Video Objective $0.32×$
1 10450528 Leica Video Objective $0.5×$
10447367 Leica Video Objective $0.63×$
1 10446307 Leica Video Objective $0.8×$

9 Image Sensor Data

Type Sensor $S_w$ $S_h$ $I_w$ $I_h$ $S_d$ $S_A$ $I_{MP}$ $P_w$ $P_h$ $P_{AR}$ $P_{IJSPAR}$ Ref
! type sensor Sw Sh Iw Ih Sd SA IMP Pw Ph PAR PIJSPAR ref
/ < > < >
1/4” IMX219 3.6800 2.760 3280 2464 4.60 10 8.1 1.122 1.120 1.00163 0.99838 IMX219
1/3.2” IMX179 3.2880 2.512 3280 2464 4.14 8 8.1 1.002 1.019 0.98328 1.01700 IMX179
1/2.5” MT9P031 5.7000 4.280 2592 1944 7.13 24 5.0 2.199 2.202 0.99883 1.00117 MT9P031
1/2.3” Leica mc170 6.1000 4.600 2592 1944 7.64 28 5.0 2.353 2.366 0.99457 1.00546 mc170
1/2.3” Leica mc190 6.1000 4.600 3648 2736 7.64 28 10.0 1.672 1.681 0.99457 1.00546 mc190
1/2.3” IMX477 RPI 6.2868 4.712 4056 3040 7.86 29 12.3 1.550 1.550 1.00000 1.00000 RPI
1/1.8” IMX334 7.9000 4.640 3952 2320 9.16 36 9.2 1.999 2.000 0.99949 1.00051 IMX334
2/3” IMX264 8.5000 7.100 2464 2056 11.08 60 5.1 3.450 3.453 0.99895 1.00105 IMX264
16mm film 10.3000 7.400 4120 2960 12.68 76 12.2 2.500 2.500 1.00000 1.00000 16mm
1” IMX183 13.1300 8.760 5472 3648 15.78 115 20.0 2.399 2.401 0.99924 1.00076 IMX183
1.1” IMX304 14.2000 10.400 4104 3006 17.60 147 12.3 3.460 3.460 1.00008 0.99992 IMX304
4/3” OMD EM1 M2 17.4000 13.000 5184 3888 21.72 226 20.2 3.356 3.344 1.00385 0.99617 OLY
APS-C Nikon D3200 23.2000 15.400 6016 4000 27.85 357 24.1 3.856 3.850 1.00166 0.99834 APSC
35mm film 36.0000 24.000 14400 9600 43.27 864 138.2 2.500 2.500 1.00000 1.00000 35mm

10 DIY RPI Camera

file:rpicam1_800.jpg

file:rpicam2_800.jpg

file:rpicam4_800.jpg

10.1 The Idea

If you have arrived here via direct link, then you might be interested to know that your browser is pointed to the middle of a larger document – my personal stereo microscope notes. While these are my personal notes, I have attempted to expand this section a bit to make it easier to follow for someone wishing to replicate my camera setup.

Microscope cameras with built in image analysis software are pretty cool. Simply connect the camera to your monitor & mouse, and you can do simple image processing and measurement without a computer. These solutions are expensive for what you get, and the analysis software is pretty limited. So I thought, why not build my own? It’s just a tiny computer and a camera in a compact case after all. If I used a Raspberry Pi, then I could actually run my favorite image analysis software (Fiji/ImageJ) right on the camera.

10.2 Bill Of Materials

ItemPrice (US $)
Raspberry Pi 4 Model B - 8 GB RAM75
Raspberry Pi 4 Pro Mounting Plate for HQ Camera7
Heatsink Raspberry Pi 4 Case with Dual Fans26
Raspberry Pi High Quality HQ Camera - 12MP50
MicroSD Card15
Micro HDMI to HDMI Cable12
CanaKit RPI 4 Power Supply with PiSwitch11
Total196

10.3 System Setup

Note: These instructions are for the Bullseye based Raspberry Pi OS relased in November of 2021!

10.3.1 Minimal Configuration

The system setup steps I used for my camera will not work for others because I made use of several aspects of my personal home directory configuration others will not have. What follows are simplified configuration steps I believe will for for most people out of the box. The only tricky bit is Fiji because it is such a dynamic project, things change.

#### Refresh packages and update everything
sudo apt-get update
sudo apt-get upgrade
sudo reboot
#### Camera packages
sudo apt install -y libcamera-apps
sudo apt install -y libcamera-dev libepoxy-dev libjpeg-dev libtiff5-dev
#### Install my favorite  packages
sudo apt install -y emacs gnuplot maxima sbcl telnet zsh tmux gitk xterm imagemagick nomacs gimp ruby exiv2 git openssl
#### Install & Setup java
sudo apt install -y openjdk-8-jdk
#### Download Fiji software & launcher
cd ~
test -e fiji-nojre.zip || wget 'https://downloads.imagej.net/fiji/latest/fiji-nojre.zip' 
test -e ImageJ.sh || wget 'https://github.com/imagej/imagej2/raw/master/bin/ImageJ.sh'
#### Unpack Fiji
unzip fiji-nojre.zip
#### Put in place ImageJ.sh script (hardwire the install directory)
sed 's/^DIRECTORY=.*/DIRECTORY=~\/Fiji.app/' ImageJ.sh > ~/Fiji.app/ImageJ.sh
chmod a+rx ~/Fiji.app/ImageJ.sh
#### Workaround for a bug in current Fiji
mv ~/Fiji.app/jars/FilamentDetector-1.0.0.jar ~/Fiji.app/jars/FilamentDetector-1.0.0.bad
#### Link ImageJ.sh into /usr/bin/ as ImageJ
sudo ln -s ~/Fiji.app/ImageJ.sh /usr/bin/ImageJ
#### Run Fiji and update *EVERYTHING*
/usr/bin/ImageJ
#### Clone the git repos
cd ~
git clone 'https://github.com/richmit/microscope.git'
git clone 'https://github.com/richmit/imagej.git'
#### Link piSnap to /bin/
sudo ln -s ~/microscope/piSnap.sh /usr/bin/piSnap
chmod a+rx /usr/bin/piSnap
### Link the RPI_tools into Fiji
ln -s ~/imagej/PhilaJ-and-RPI_Tools/RPI_tools.ijm ~/Fiji.app/macros/toolsets/RPI_tools.ijm

10.3.2 My Configuration

Most Unix/Linux users have pretty strong opinions on how to setup a personal working environment. Emacs vs VI anyone? This section documents my personal configuration and is pretty specific to my operating environment. Some differences from the ”Minimal Configuration” section above:

  • Makes use of scripts and data found in my home directory
  • Uses my environment setup scripts to put piSnap.sh in the right place and link it.
  • ~/bin is where the binaries go
  • I use my preferred login name for the main account, and remove the ’pi’ user from the system
  • Quite a bit more apt installed software (Emacs, sbcl, maxima, gnuplot, paraview, etc…)
  • I install the free42 calculator along with some software on the calculator itself.
  • My primary system for photography and image analysis is a Windows system
    • This system has a nice, color corrected 4K monitor, and a couple scanners attached
    • Some of the software I use is proprietary and only runs on Windows
    • With regard to free software, I run mostly the same stack on Windows (Fiji, GIMP, Imagemagick, Emacs, etc…) in MSYS2

10.3.2.1 System Setup

#### Refresh packages and update everything
sudo apt-get update
sudo apt-get upgrade
#### DO: Turn off auto login for pi user
#### DO: Turn on SSH & VNC
sudo reboot
#### Camera packages
sudo apt install -y libcamera-apps
sudo apt install -y libcamera-dev libepoxy-dev libjpeg-dev libtiff5-dev
sudo apt install -y qtbase5-dev libqt5core5a libqt5gui5 libqt5widgets5 qtbase5-dev libqt5core5a libqt5gui5 libqt5widgets5
sudo apt install -y python3-pip libboost-dev libgnutls28-dev openssl meson libglib2.0-dev libgstreamer-plugins-base1.0-dev
#### Install my favorite  packages
sudo apt install -y emacs gnuplot maxima sbcl telnet zsh tmux gitk xterm imagemagick nomacs gimp ruby exiv2
#### Install & Setup java
sudo apt install -y openjdk-8-jdk
#### Make local links
for f in ruby perl sbcl; do
  if [ -e /usr/bin/$f ]; then
    sudo ln -s /usr/bin/$f /usr/local/bin/$f
  else
    echo Missing: /usr/bin/$f
  fi
done
#### Create my account
sudo addgroup richmit
sudo adduser --gid 1001 richmit ## use GID from previous command
#### Add me to all the groups the pi user is in -- or at least users that start with pi ;)
sudo usermod -aG `grep '[:,]pi' /etc/group | cut -d: -f3 | tr '[:space:]' , | sed 's/,$//'` richmit
#### Change my shell
sudo usermod -s /usr/bin/zsh richmit
#### Change root's password
sudo passwd root
#### Fix the caps lock key
sudo sh -c 'sed "s/^XKBOPTIONS=.*/XKBOPTIONS=\"ctrl:nocaps\"/" < /etc/default/keyboard > /etc/default/keyboard.new'
sudo chmod a+r /etc/default/keyboard /etc/default/keyboard.new
if diff -q /etc/default/keyboard /etc/default/keyboard.new; then sudo rm /etc/default/keyboard.new; else sudo mv /etc/default/keyboard /etc/default/keyboard.bak_`date +%s`; sudo mv /etc/default/keyboard.new /etc/default/keyboard; fi
#### DO: Add my account to sudo
#### Login with my new account
sudo su - richmit
#### Setup directories & links in $HOME
cd ~
mkdir -p ~/bin
mkdir -p ~/tmp/tmux/sockets
mkdir -p ~/Pictures/pi-cam
mkdir -p ~/synced/world/pi-data/
mkdir -p ~/synced/world/dotfiles/
mkdir -p ~/synced/world/dotfilesSecure/
mkdir -p ~/synced/world/stuff/homeNetwork/
mkdir -p ~/synced/world/stuff/my_ref/
mkdir -p ~/synced/world/stuff/notes/
mkdir -p ~/synced/world/my_prog/learn/ex-ruby/
mkdir -p ~/synced/world/my_prog/lispStuff/lispy/
mkdir -p ~/synced/world/my_prog/MJRdebianPakageTools/
mkdir -p ~/synced/world/my_prog/tmuxStuff/
mkdir -p ~/synced/world/my_prog/UNIXutils/
mkdir -p ~/synced/world/my_prog/utils/
mkdir -p ~/synced/world/my_prog/microscope
mkdir -p ~/synced/world/my_prog/ImageJ
mkdir -p ~/synced/world/my_prog/mpms
mkdir -p ~/synced/world/my_prog/dir-inventory/
mkdir -p ~/synced/core/
mkdir -p ~/synced/Doc2/gadgets/leica_microscopes/
ln -s ~/synced/world ~/world
ln -s ~/synced/core ~/core
#### DO: Sync data from laptop via rsync
#### Setup dotfiles & ~/bin
./world/my_prog/UNIXutils/SelectSetup.rb --loc=HOME; ./world/my_prog/UNIXutils/SetupBin.rb
#### DO: Reboot
#### DO: Login as myself
#### Delete pi user
sudo userdel -r pi
#### DO: Enable automatic login
#### DO: Change hostname to pi-cam
#### DO: Reboot
#### Download Fiji software & launcher
cd ~
test -e fiji-nojre.zip || wget 'https://downloads.imagej.net/fiji/latest/fiji-nojre.zip' 
test -e ImageJ.sh || wget 'https://github.com/imagej/imagej2/raw/master/bin/ImageJ.sh'
#### Unpack Fiji
unzip fiji-nojre.zip
#### Put in place ImageJ.sh script (hardwire the install directory)
sed 's/^DIRECTORY=.*/DIRECTORY=~\/Fiji.app/' ImageJ.sh > ~/Fiji.app/ImageJ.sh
chmod a+rx ~/Fiji.app/ImageJ.sh
#### Workaround for a bug in current Fiji
mv ~/Fiji.app/jars/FilamentDetector-1.0.0.jar ~/Fiji.app/jars/FilamentDetector-1.0.0.bad
#### Run Fiji and update
~/Fiji.app/ImageJ.sh
### Link the RPI_tools into Fiji
ln -s ~/world/my_prog/imagej/PhilaJ-and-RPI_Tools/RPI_tools.ijm ~/Fiji.app/macros/toolsets/RPI_tools.ijm
### Link the PhilaJ into Fiji
ln -s ~/world/my_prog/imagej/PhilaJ-and-RPI_Tools/PhilaJ.ijm ~/Fiji.app/macros/toolsets/PhilaJ.ijm
#### Setup dotfiles & ~/bin -- this time to put ImageJ.sh & ImageJ into ~/bin
./world/my_prog/UNIXutils/SelectSetup.rb --loc=HOME; ./world/my_prog/UNIXutils/SetupBin.rb
#### DO: Add ImageJ.sh to launch menu -- icon in ~/core/icons
#### Install free42 calculator
cd ~
rm -rf ~/free42
git clone 'https://github.com/thomasokken/free42.git'
cd free42/gtk
make BCD_MATH=1 AUDIO_ALSA=1
sudo cp free42dec /usr/local/bin/free42-3.0.6
sudo rm -f /usr/local/bin/free42
sudo ln -s /usr/local/bin/free42-3.0.6 /usr/local/bin/free42
#### DO: Add free42 to launch menu -- icon in ~/core/icons
#### DO: Add piSleep to launch menu -- icon in ~/core/icons
#### DO: Logout
#### DO: Login

10.3.2.2 System Sync

I use rsync to keep data in sync between my camera and primary workstation.

date; echo back-dat-sync;        rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2                  --rsh='ssh' pi-cam.home.mitchr.me:synced/pi-data/                              /c/Users/richmit/Documents/world/pi-cam/;
date; echo back-pic-sync;        rsync -rlt --log-format=%f                            --modify-window=2                  --rsh='ssh' pi-cam.home.mitchr.me:Pictures/pi-cam/                             /c/Users/richmit/Pictures/pi-cam/;
date; echo microscope-code;      rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/microscope/               pi-cam.home.mitchr.me:synced/world/my_prog/microscope/;
date; echo imagej-code;          rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/imagej/                   pi-cam.home.mitchr.me:synced/world/my_prog/imagej/;
date; echo dotfiles;             rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/dotfiles/                         pi-cam.home.mitchr.me:synced/world/dotfiles/;
date; echo dotfilesSecure;       rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/dotfilesSecure/                   pi-cam.home.mitchr.me:synced/world/dotfilesSecure/;
date; echo homeNetwork;          rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/stuff/homeNetwork/                pi-cam.home.mitchr.me:synced/world/stuff/homeNetwork/;
date; echo my_ref;               rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/stuff/my_ref/                     pi-cam.home.mitchr.me:synced/world/stuff/my_ref/;
date; echo notes;                rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/stuff/notes/                      pi-cam.home.mitchr.me:synced/world/stuff/notes/;
date; echo mpms;                 rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/mpms/                     pi-cam.home.mitchr.me:synced/world/my_prog/mpms/;
date; echo dir-inventory;        rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/dir-inventory/            pi-cam.home.mitchr.me:synced/world/my_prog/dir-inventory/;
date; echo ruby-examples;        rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/learn/ex-ruby/            pi-cam.home.mitchr.me:synced/world/my_prog/learn/ex-ruby/;
date; echo lispy;                rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/lispStuff/lispy/          pi-cam.home.mitchr.me:synced/world/my_prog/lispStuff/lispy/;
date; echo MJRdebianPakageTools; rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/MJRdebianPakageTools/     pi-cam.home.mitchr.me:synced/world/my_prog/MJRdebianPakageTools/;
date; echo tmuxHelper;           rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/tmuxHelper/               pi-cam.home.mitchr.me:synced/world/my_prog/tmuxHelper/;
date; echo UNIXutils;            rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/UNIXutils/                pi-cam.home.mitchr.me:synced/world/my_prog/UNIXutils/;
date; echo utils;                rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/world/my_prog/utils/                    pi-cam.home.mitchr.me:synced/world/my_prog/utils/;
date; echo core;                 rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/core/                                   pi-cam.home.mitchr.me:synced/core/;
date; echo leicaS8APO-docs;      rsync -rlt --log-format=%f --delete --delete-excluded --modify-window=2 --exclude '.git' --rsh='ssh' /c/Users/richmit/Documents/reading/Doc2/gadgets/leica_microscopes/ pi-cam.home.mitchr.me:synced/Doc2/leica_microscopes/;
date

10.4 RPI Software

My goals:

  • ImageJ/Fiji
    • Capture images directly from ImageJ/Fiji so I can immediately preform an image analysis
    • Setting image scale needs to be easy because measuring lengths is my #1 application
    • Identical UI between Windows and RPI
    • The software should be fully integrated into PhilaJ (an extensive set of ImageJ/Fiji macros for philatelic image analysis)
    • The microscope functionality should be available without the bulk of the PhilaJ user interface for people not interested in philately.
  • CLI
    • Needs to integrate will with ImageJ/Fiji so that it is easy to load them in ImageJ/Fiji later
    • Completely indipendant of the ImageJ/Fiji software
    • As simple as possible with minimal external requirements – just the RPI CLI image tools and basic shell stuff
  • General Requirements
    • Optionally show a preview before capture
    • See a live view from the camera & control the size of the preview
    • Capture sequences of related images, and name so they are grouped together
    • Put captured images in a known directory with a standard naming convention so that it is simple to orginize and sync data between camear and computers

10.4.1 RPI Image Capture Script

This script is pretty simple. It provides a way to capture one or more images outside of ImageJ/Fiji, but in a way compatible with the ImageJ/Fiji macros provided below. I almost always have ImageJ/Fiji running on my camera, so I don’t end us uping this cript much; however, it is still nice to have around.

Take a snapshot using the Raspberry Pi HQ Camera and save it in a standard way

Use: piSnap.sh [options]
  Options:
    -p        Preview!  No images are captured. Other arguments are ignored
    -k        Show a preview, and capture when [enter] is pressed.
              Without -k an image is immediatly captured with no preview
    -s        Show image after capture with nomacs
    -a ANNO   Annotation: Used to identify the capture.
              Adds a "-ANNOTATION" component to the captured filename.
              See the "File Names" section below
    -g GROUP  Group name -- used for grouping similar captures.
              Adds a "_GROUP" component to the captured filename
              See the "File Names" section below
    -v        Verbose mode
    -f        Fake Capture Mode that uses convert instead of libcamera-still
              Used for debugging.  Most useful when combined with -v.
    -b BIN    Full path to the libcamera-still binary
              Default: /usr/bin/libcamera-still
    -d DIR    Directory to store captured images.
              Default: $HOME/Pictures/pi-cam
              Note: The related ImageJ/Fiji macro expects the default value!
    -e ENC    File format: jpg, bmp, gif, png, rgb
              Default: jpg
  File Names
    Image names are like: YYYYMMDDHHMMSS_GROUP-ANNOTATION.ENC
                          |              |     |
                          |              |     File Annoation
                          |              Group Name
                          date/time stamp
      - The "_GROUP" component of the name will not be pressent
        if the -g option was not provided.
      - The "-ANNOTATION" component of the name will not be pressent
        if the -a option was not provided.
      - The -a and -g arguments are translated automatically into
        something suitable:
          - Non-alphanumeric characters are converted to underscores.
          - Leading underscores and dashes are removed
          - The -g argument has all dashes removed

Part of the setup instructions above install this script.

The script can be found on github: https://github.com/richmit/microscope

10.4.2 ImageJ/Fiji Toolset/Macros

The ImageJ/Fiji toolset, called ”RPI_tools”, is actually a direct copy my "PhilaJ" software with an alternative, stripped down user interface that only exposes the microscope functionality. That is to say, the only difference between ”RPI_tools” and ”PhilaJ” is the ImageJ/Fiji toolset code the exposes the functionality to the end user. Full documentation may be found here:

https://richmit.github.io/imagej/PhilaJ.html#rpi-tools

The setup instructions above install this package into Fiji. You can find the code on github:

https://github.com/richmit/imagej