NIS-Elements to Piximetre

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myxomop
Posts: 55
Joined: Wed Jul 11, 2012 11:22 am
Location: New York
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NIS-Elements to Piximetre

Post by myxomop »

I just shot a bunch of micrographs on a big, fancy Nikon Eclipse 80i w/ DIC. They were captured via Nikon's NIS-Elements software and saved as .tiff files. I did not have much time to take measurements, and am now wondering if there is a way to do so after the fact with Piximetre rather than with prohibitively expensive Nikon software.

I've discovered that the NIS-Elements Viewer (free) is able to put up a scale bar based on the calibration data baked into the image metadata (.05?m/px), but when the same image is loaded into Piximetre, an error appears stating the image does not contain the necessary metadata.

Below is a sample image:

https://drive.google.com/open?id=1LXDnJ ... igxBf_NxJM

Any and all help greatly appreciated.

-myxomop
Last edited by myxomop on Sat Apr 28, 2018 10:51 am, edited 1 time in total.
MACRO:
Canon 6D, Canon MP-E 65mm Macro Lens, Sigma 50mm f/2.8 EX DG Macro, Amazon.com : YongNuo YN-14EX TTL Macro Ring Lite Flash, Laowa/Venus Optics KX-800 Flexible Macro Twin Flash, Gitzo GT2540EX Tripod, Acratech GV2 Ballhead

MICRO:
Trinocular Olympus BHS, SPlan 4x, 10x, 20x, 40x (1.25 N.A.), SPlanApo 100x Oil (1.4 N.A.), BH2-AAC Aplanatic-Achromatic 1.4 N.A Brightfield Condenser, WHK 10x 20 L Eyepieces, NFK 2.5× LD 125 Photo Eyepiece, Diagnostic Instruments PA1-10A SLR Camera Adapter

JohnyM
Posts: 463
Joined: Tue Dec 24, 2013 7:02 am

Post by JohnyM »

How about using FIJI / ImageJ ?

zzffnn
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Location: Boston, Massachusetts, USA
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Post by zzffnn »

You may not need any software.

Just use a microscope stage micrometer with micron size marks. Measure the entire view field captured through each objective, in microns, then calculate actual subject size based on its relative size compared to entire view field.

For example, if your 40x objective captures 300 microns in the widest dimension, and your subjective takes 50% of that dimension, then your subject length is 150 microns.

Another way is image a 1 or 2 micron length of stage micrometer, with each objective, then use (overlay) that image as a ruler.

myxomop
Posts: 55
Joined: Wed Jul 11, 2012 11:22 am
Location: New York
Contact:

Post by myxomop »

zzffnn wrote:You may not need any software.

Just use a microscope stage micrometer with micron size marks. Measure the entire view field captured through each objective, in microns, then calculate actual subject size based on its relative size compared to entire view field.

For example, if your 40x objective captures 300 microns in the widest dimension, and your subjective takes 50% of that dimension, then your subject length is 150 microns.

Another way is image a 1 or 2 micron length of stage micrometer, with each objective, then use (overlay) that image as a ruler.
I normally calibrate Piximetre with one or more shots of a stage micrometer at whatever magnifications I want calibrated, but there wasn't one available to me this time, and I figured that for all the bells and whistles this software has, it wouldn't be unrealistic to expect the metadata to contain everything that a program like Piximetre would need to be calibrated automatically. I was, apparently, mistaken :(
MACRO:
Canon 6D, Canon MP-E 65mm Macro Lens, Sigma 50mm f/2.8 EX DG Macro, Amazon.com : YongNuo YN-14EX TTL Macro Ring Lite Flash, Laowa/Venus Optics KX-800 Flexible Macro Twin Flash, Gitzo GT2540EX Tripod, Acratech GV2 Ballhead

MICRO:
Trinocular Olympus BHS, SPlan 4x, 10x, 20x, 40x (1.25 N.A.), SPlanApo 100x Oil (1.4 N.A.), BH2-AAC Aplanatic-Achromatic 1.4 N.A Brightfield Condenser, WHK 10x 20 L Eyepieces, NFK 2.5× LD 125 Photo Eyepiece, Diagnostic Instruments PA1-10A SLR Camera Adapter

myxomop
Posts: 55
Joined: Wed Jul 11, 2012 11:22 am
Location: New York
Contact:

Post by myxomop »

JohnyM wrote:How about using FIJI / ImageJ ?
I DLed and installed Fiji/ImageJ2, but have found it to be a much more complicated piece of software than Piximetre, which is pretty much exclusively for making measurements. I would greatly prefer sticking with that program unless 1) ImageJ2 can read the NIS .tiffs' calibration metadata (I don't think it can), and 2) there is some tutorial on how to perform the simple measuring tasks I would normally user Piximetre for.
MACRO:
Canon 6D, Canon MP-E 65mm Macro Lens, Sigma 50mm f/2.8 EX DG Macro, Amazon.com : YongNuo YN-14EX TTL Macro Ring Lite Flash, Laowa/Venus Optics KX-800 Flexible Macro Twin Flash, Gitzo GT2540EX Tripod, Acratech GV2 Ballhead

MICRO:
Trinocular Olympus BHS, SPlan 4x, 10x, 20x, 40x (1.25 N.A.), SPlanApo 100x Oil (1.4 N.A.), BH2-AAC Aplanatic-Achromatic 1.4 N.A Brightfield Condenser, WHK 10x 20 L Eyepieces, NFK 2.5× LD 125 Photo Eyepiece, Diagnostic Instruments PA1-10A SLR Camera Adapter

JohnyM
Posts: 463
Joined: Tue Dec 24, 2013 7:02 am

Post by JohnyM »

ImageJ and especially FIJI is loaded with specialist tools. It's definately not an amateur aimed program. AFAIK FIJI can read pretty much everything, including confocal scopes metadata, so it's worth a try (and research how-to).
Measurements have many options. Simplest way (not necessarly best) is to click:
-Analyze
-Set scale (type numbers from your metadata here)
After that use any of marking tools. You get measurement displayed live in program bar, and after you've selected what you want press CTRL+M and you get excel format data.

It might sound complicated but it's literally 3 clicks.

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