Looking for an app for morphological analysis of microscope images...

[a a]

Looking for an app for morphological analysis of microscope images
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I have found on the net applications for the analysis of cell images under the microscope, for the analysis of blood smear, but they work with hardware
and I am looking for an off-line application that will work with image files from the microscope.

It could be for a smartphone, it could be a developer\'s version , it could work in the cloud, but whatever I am looking for to find, so that I don\'t buy an electron microscope or other for testing along with it.

 

[Anthony William Sloman]

On Thursday, October 20, 2022 at 7:57:32 AM UTC+11, a a wrote:

Looking for an app for morphological analysis of microscope images
34 views
Subscribe
21:29 (1 hour ago)
to
I have found on the net applications for the analysis of cell images under the microscope, for the analysis of blood smear, but they work with hardware
and I am looking for an off-line application that will work with image files from the microscope.

It could be for a smartphone, it could be a developer\'s version , it could work in the cloud, but whatever I am looking for to find, so that I don\'t buy an electron microscope or other for testing along with it.

Electron microscopes aren\'t much good for looking at biological specimens. The specimens don\'t like a hard vacuum. \"Environmental\" electron microscopes do offer a compromise.

Confocal optical microscopes do better, and there are tricks - like \"hole burning\" that let you do better still.

--
Bill Sloman, Sydney

 

[John Walliker]

On Thursday, 20 October 2022 at 04:55:06 UTC+1, bill....@ieee.org wrote:

On Thursday, October 20, 2022 at 7:57:32 AM UTC+11, a a wrote:
Looking for an app for morphological analysis of microscope images
34 views
Subscribe
21:29 (1 hour ago)
to
I have found on the net applications for the analysis of cell images under the microscope, for the analysis of blood smear, but they work with hardware
and I am looking for an off-line application that will work with image files from the microscope.

It could be for a smartphone, it could be a developer\'s version , it could work in the cloud, but whatever I am looking for to find, so that I don\'t buy an electron microscope or other for testing along with it.
Electron microscopes aren\'t much good for looking at biological specimens. The specimens don\'t like a hard vacuum. \"Environmental\" electron microscopes do offer a compromise.

Confocal optical microscopes do better, and there are tricks - like \"hole burning\" that let you do better still.

Transmission electron microscopes can be extremely valuable for looking at
biological specimens that have been sliced up into very thin sections and stained with
nasty materials like osmium tetroxide or uranium acetate. My wife spent many years
doing such things. One of her images was used in Gray\'s Anatomy.
Scanning electron microscopes also have their uses, especially for producing nice looking
pictures with huge depth of focus. However, they are generally only good for looking
at surfaces (although internal views can be obtained by looking at fracture surfaces).
I\'ve done some SEM work, but not on biological specimens. The microscope I was using
was mainly intended for biological work however.
Confocal optical microscopy is a very clever and effective technique which can
be used on living material.

As for the question asked by the OP - it is impossible to give a useful answer without
knowing what he is trying to discover and where his images are going to come from.
Automated and computer-assisted image analysis has been around for many decades,
but is very much tailored to answering specific questions.

John

 

[Anthony William Sloman]

On Thursday, October 20, 2022 at 8:20:48 PM UTC+11, John Walliker wrote:

On Thursday, 20 October 2022 at 04:55:06 UTC+1, bill....@ieee.org wrote:
On Thursday, October 20, 2022 at 7:57:32 AM UTC+11, a a wrote:

<snip>

As for the question asked by the OP - it is impossible to give a useful answer without
knowing what he is trying to discover and where his images are going to come from.
Automated and computer-assisted image analysis has been around for many decades,
but is very much tailored to answering specific questions.

The one thing we know about the original poster is that it is a waste of time responding to him. He\'s an idiot, and unpleasant with it.

I figure it is worth posting responses that highlight the defective nature of his questions, but that isn\'t going top help him - ]he\'s beyond help.

--
Bill Sloman, Sydney

 

[a a]

#shutupyoustupiddogfromsydney

you don\'t know the answer

 

[Anthony William Sloman]

On Thursday, October 20, 2022 at 9:59:54 PM UTC+11, a a wrote:

> you don\'t know the answer

You can\'t ask a question to which there is a sensible answer. There is a sensible response, but you aren\'t gong to bother to learn more about the subject that you think you are asking questions about, not that it looks as if you could.

--
Bill Sloman, Sydney

 

[Anthony Stewart]

and I am looking for an off-line application that will work with image files from the microscope.

It could be for a smartphone, it could be a developer\'s version , it could work in the cloud,

You will be unable to find anything with this description.

You must specify File formats and user experience, UX, and some user enhancement options.

The most common medical imaging offline app is used for MRI, CT etc. is DICOM and is included with all patient records if requested on CD\'s https://www.microdicom.com/

 

[a a]

On Thursday, 20 October 2022 at 22:42:07 UTC+2, Anthony Stewart wrote:

and I am looking for an off-line application that will work with image files from the microscope.

It could be for a smartphone, it could be a developer\'s version , it could work in the cloud,
You will be unable to find anything with this description.

You must specify File formats and user experience, UX, and some user enhancement options.

The most common medical imaging offline app is used for MRI, CT etc. is DICOM and is included with all patient records if requested on CD\'s https://www.microdicom.com/
You mean old technology in medical image viewing, old data formats.

Early 2020 I got trained in covid detection, prevention, treatment in Wuhan
and a single doctor diagnosed 200 covid patients per shift with high-tech live 3D image processing CT.

But I am interested in morphological detection of objects, features in sample medical images

 

[server]

Fiji Image-J

https://fiji.sc/

 

[a a]

On Thursday, 20 October 2022 at 23:26:12 UTC+2, Wand...@noplace.com wrote:

Fiji Image-J

https://fiji.sc/

thank you,
excellent
just learning and testing examples

 

[a a]

On Friday, 21 October 2022 at 00:11:47 UTC+2, a a wrote:

On Thursday, 20 October 2022 at 23:26:12 UTC+2, Wand...@noplace.com wrote:
Fiji Image-J

https://fiji.sc/
thank you,
excellent
just learning and testing examples
There are tens of other image processing applications/ tools, promoted by Fiji

We need to arrange for on-line conference on image processing to build report discussing every image processing application, appended by images showing features processed.




AGAVE
AICSImageIO
Aydin
BIAFLOWS
BIII
BiofilmQ
Bio-Formats
BoneJ
BrainGlobe
Cellpose
CellProfiler
CLIJ
CytoMAP
Cytomine
DeepLabCut
Fiji
FLIMLib
GerBI
Icy
IDR
ilastik
ImageJ
ImageJ2
ImgLib2
ImJoy
JIPipe
Mars
MCMICRO
MIA
MIB
μManager
MoBIE
MorphoGraphX
MorphoNet
napari
NEUBIAS
OME
OMERO
OmeSliCC
OpenIRIS
OpenSPIM
Orbit
Piximi
PYME
Python-Microscope
QuPath
SCIFIO
scikit-image
sciview
SR-Tesseler
StarDist
starfish
TissUUmaps
vedo
webKnossos
ZeroCostDL4Mic

 

[John Walliker]

On Friday, 21 October 2022 at 12:25:53 UTC+1, a a wrote:

We need to arrange for on-line conference on image processing to build report
discussing every image processing application, appended by images showing
features processed.

You still haven\'t given anyone a clue about what you are trying to discover. Without that,
discussion is futile. Image processing software is a tool. So is a microscope.
You would not expect us to advise on the relative merits of hammers
and screwdrivers if you did not tell us whether you were planning to knock a wall
down or fix a clock.

John

 

[CCP Spy found]

a a <manta103g@gmail.com> wrote:

Early 2020 I got trained in covid detection, prevention, treatment in
Wuhan

This reveal explains a lot. We have our own assigned Chinese Communist
Party spy/disruptor in A a manta103g@gmail.com.

This explains the rampant stupidity, the overt pushing of CCP
propaganda, the inability to form coherent English phrases (much less
coherent English sentences).

For some reason, the CCP has assigned one of their operatives (a a) to
this group to sow disruption and discontent everywhere.

For the Chinese Communist Party spy, here are some suggested readings:

1989 Tiananmen Square protests and massacre
https://en.wikipedia.org/wiki/1989_Tiananmen_Square_protests_and_massacre

Free Tibet
https://freetibet.org/

What is happening with the Uighurs in China
https://www.pbs.org/newshour/features/uighurs/

 

[CCP]

John Walliker <jrwalliker@gmail.com> wrote:

On Friday, 21 October 2022 at 12:25:53 UTC+1, a a wrote:

We need to arrange for on-line conference on image processing to
build report discussing every image processing application, appended
by images showing features processed.

You still haven\'t given anyone a clue about what you are trying to
discover. Without that, discussion is futile. Image processing
software is a tool. So is a microscope. You would not expect us to
advise on the relative merits of hammers and screwdrivers if you did
not tell us whether you were planning to knock a wall down or fix a
clock.

Given that the A a troll has outed itself as a Chinese Communist Party
operative:

http://al.howardknight.net/?ID=166635977100
http://al.howardknight.net/?ID=166636053700

this is not at all unexpected. The disruption sowed by a vague
question with multiple possible answers and no way to provide any
useful specifics, and no explanation when asked, is right out of a CCP
disruptor\'s playbook.

 

[server]

FIJI stands for Fiji Is Just Image-J

I used it to test CCD cameras and to create anaglyph images from old stereo pictures you can find on the internet.

It has plug-ins for morphological analysis.

https://imagej.net/plugins/morpholibj

https://imagej.net/plugins/morphological-segmentation

If you wish to test other programs and submit to us a report, feel free to do so. It would be a better of your time than posting news links.

 

[a a]

On Friday, 21 October 2022 at 16:06:49 UTC+2, Wand...@noplace.com wrote:

FIJI stands for Fiji Is Just Image-J

I used it to test CCD cameras and to create anaglyph images from old stereo pictures you can find on the internet.

It has plug-ins for morphological analysis.

https://imagej.net/plugins/morpholibj

https://imagej.net/plugins/morphological-segmentation

If you wish to test other programs and submit to us a report, feel free to do so. It would be a better of your time than posting news links.
thank for your excellent plug-in links for morphological analysis.

I plan to hold global conference on Image Processing Technologies in Medicine, Astronomy, Physics, Biology ....
Live Posters in Zero-Click Technology, supported by live/ off-line chat

I would like to implement Voice-Control in image processing, since number of options, which can be selected goes into hundreds.

Fiji promotes about 60 image processing applications, developed by third parties
and it\'s virtually impossible to download and test every one and select thousands of options by mouse clicks.

So I plan to hold State-of-the-Art in Image Processing Conference to makes things quick

Morphological plugins, mentioned above, are exactly fit to be voice controlled/ operated.

Examples are excellent

1.
\"Principle of morphological dilation and erosion on a binary set, using a disk-shaped structuring element.

(comes from Matlab)

2.
\"Some examples of morphological filters on a grey level image. From left to right: original image, result of dilation with a square structuring element, and result of erosion with the same structuring element.

3.
\"Some examples of composed morphological filters. From left to right: morphological closing, and morphological opening.

4.
\"More examples of composed morphological filters. From left to right: morphological gradient, morphological Laplacian, morphological white top-hat.

5.
\"Filtering of a thin structure. (a) Original image representing apple cells observed with confocal microscopy. The application of a Gaussian filter (b) or median filter (c) results in noise reduction, but also in a loss of the signal along the cell walls. The directional filtering (d) better preserves the thickness of the structure.

(images are too small to detect any difference)

6.
\"Principle of directional filtering of a thin structure. (a) and (b): result of median filter using an horizontal and a vertical linear structuring element. (c) and (d): combination of the results obtained from two directions (horizontal and vertical) and four directions (by adding diagonal directions).

(images are too small)

7.
\"MorphoLibJ filter examples: DAPI stained nuclei image and the result of applying different morphological filters with an octagon of radius 5 as structuring element.

???

8.
\"Principle of the geodesic reconstruction algorithm. From left to right: original image in gray with marker superimposed in black, and result of conditional dilations with increasing sizes.

(interesting feature)

9.
\"Some applications of geodesic reconstruction. From left to right: original image, result of kill borders, result of fill holes.

(kill borders filter is not intuitive but removes objects sticked to borders of the image)

10.
\"Some applications of geodesic reconstruction on grey level images. From left to right: original image with superimposed markers, result of geodesic reconstruction by dilation, result of border kill operation.

(not sure, geodesic reconstruction stays for what)


11.
\"Regional and extended maxima on a grey-level image. Left: original image. Middle: result of regional maxima. Right: result of extended maxima.

12.
\"Example of area opening on a binary image. Left: original binary image. Middle: identification of connected components. Right: only the connected components with a sufficient size (defined by the area), have been retained.

(area calculation, detection, sorting by size for postprocessing)

13.
\"Example of area opening on a grayscale image. Left: original grayscale image of a leaf (image courtesy of Eric Biot, INRA Versailles). Middle: grayscale size opening making bright spots disappear. Right: comparison with morphological closing with square structuring element of radius 1: bright spots are removed, but some veins also disappear.

(small images are not clean for visual inspection)


14.
\"Overlay of watershed lines on blurred blobs.

(interesting visual effect)

15.
\"Illustration of Euler Number definition. Left: three particles with Euler numbers equal to 1, 0 and -1, respectively. Right: example of a 3D particle with an Euler number equal to -1, corresponding to the subtraction of 1 connected components minus two handles.

(complicated)


16.
\"Computation of perimeter and geodesic diameter. Left: principle of perimeter estimation by counting intersections with set of lines. Right: illustration of the geodesic diameter measured on a non convex particle.

17.
\"Computation of the geodesic diameter on a segmented image from the DRIVE database (Staal et al., 200414). Each connected component was associated to a label, then the longest geodesic path within each connected component was computed and displayed as red overlay.

(short segments in red stay for what ? )

18.
\"Computation of the Region Adjacency Graph on a microscopy image of plant tissue. Left: original image. Middle: result of watershed segmentation. Right: overlay of edges representing adjacent regions.

(left image resembles image generated by my laser pointer)

19.
\"Binary image, and result of computation of the distance transform.

(nice)

20.
\"Computation of the geodesic distance map on a binary image from the DRIVE database (Staal et al., 200414). Left: original image with marker superimposed in red. Right: result of geodesic distance map, hot colors correspond to large distances, cold colors correspond to small distances.

(nice)

21.
\"Binary image, result of connected components labeling, and computation of distance map on the complement of binary image.

(nice but not intuitive)

22.
\"Assign result of a measurement to a label image. In this example, the elongation is represented using a color code, between dark purple (circular) to yellow (very elongated).

23.
\"Assign result of a measurement to a label image. In this example, the elongation is represented using a color code, between dark purple (circular) to yellow (very elongated).

(elongation is not clearly represented in case of objects sticked to to borders of the image)

24.
\"MorphoLibJ utilities for label images. From left to right: original label image, remove border labels, remove largest region, apply size opening for keeping only regions with at least 150 pixels.

(complicated)

25.
\"Label Edition plugin overview.

(not intuitive)

26.
\"From left to right: input label image, script output, smoothed label surfaces and example of individually translated surfaces in the 3D viewer.

(???)

27.
\"

 

[a a]

On Friday, 21 October 2022 at 16:06:49 UTC+2, Wand...@noplace.com wrote:

FIJI stands for Fiji Is Just Image-J

I used it to test CCD cameras and to create anaglyph images from old stereo pictures you can find on the internet.

It has plug-ins for morphological analysis.

https://imagej.net/plugins/morpholibj

https://imagej.net/plugins/morphological-segmentation

If you wish to test other programs and submit to us a report, feel free to do so. It would be a better of your time than posting news links.
Morphological Segmentation

https://imagej.net/plugins/morphological-segmentation

1.
(first animated image complicated - no description)

2.
\"Morphological Segmentation is an ImageJ/Fiji plugin that combines morphological operations, such as extended minima and morphological gradient, with watershed flooding algorithms to segment grayscale images of any type (8, 16 and 32-bit) in 2D and 3D.

(image - complicated - not intuitive)

3.
\"You should select:

Border Image: if your input image has highlighted object boundaries.
Object Image: if the borders of the objects do not have higher intensity values than the rest of voxels in the image.


4.
\"Examples of the 4 different display options

(interesting but complicated)

5.
\"Quick start guide

This introductory screencast (which needs audio) explains the basic use of the plugin:

(thank you)

6.
\"Segmentation of a 3D image

This video tutorial (with audio as well) shows how to use the plugin segment a 3D image (confocal image of an Arabidopsis thaliana embryo, courtesy of Jean-Christophe Palauqui (INRA-Versailles)):

(high-tech - complicated)

7.
\"3d reconstruction of an *Arabidopsis thaliana* embryo using the Morphological Segmentation plugin. Image courtesy of Jean-Christophe Palauqui (INRA-Versailles)

(nice)

 

[Anthony William Sloman]

On Saturday, October 22, 2022 at 3:51:08 AM UTC+11, a a wrote:
> On Friday, 21 October 2022 at 16:06:49 UTC+2, Wand...@noplace.com wrote:

<snip>

I plan to hold global conference on Image Processing Technologies in Medicine, Astronomy, Physics, Biology ....
Live Posters in Zero-Click Technology, supported by live/ off-line chat

<snip>

Somebody is suffering from delusions of grandeur. I\'m been marking a a\'s posts as spam for months now and this promises lots more of the same. If he advertised it explicitly as comedy, he might get some takers.

--
Bill Sloman, Sydney

 

[John Walliker]

On Saturday, 22 October 2022 at 04:33:26 UTC+1, bill....@ieee.org wrote:

On Saturday, October 22, 2022 at 3:51:08 AM UTC+11, a a wrote:
On Friday, 21 October 2022 at 16:06:49 UTC+2, Wand...@noplace.com wrote:
snip
I plan to hold global conference on Image Processing Technologies in Medicine, Astronomy, Physics, Biology ....
Live Posters in Zero-Click Technology, supported by live/ off-line chat
snip

Somebody is suffering from delusions of grandeur. I\'m been marking a a\'s posts as spam
for months now and this promises lots more of the same. If he advertised it explicitly as
comedy, he might get some takers.

Indeed. I know several people who have been working for decades in just the
medical image processing and analysis area. I met people who were working on
automated analysis of bubble chamber images in 1978. Even then there was a
large body of knowledge about image processing. This is hardly a field where
somebody with no relevant knowledge can organise a conference and expect to
achieve anything. I don\'t quite understand how he will find the time when there is
all that work going on to monitor undetectable X-rays from the sun and various other
projects.

John

 

[Anass Luca]

Anthony William Sloman <bill.sloman@ieee.org> wrote:

On Saturday, October 22, 2022 at 3:51:08 AM UTC+11, a a wrote:
On Friday, 21 October 2022 at 16:06:49 UTC+2, Wand...@noplace.com wrote:

snip

I plan to hold global conference on Image Processing Technologies in
Medicine, Astronomy, Physics, Biology .... Live Posters in
Zero-Click Technology, supported by live/ off-line chat

snip

Somebody is suffering from delusions of grandeur. I\'m been marking a
a\'s posts as spam for months now and this promises lots more of the
same.

While you are marking A a\'s posts as spam, you might consider also
adding the Fred Bloggs troll and your good buddy Gnatguy to that list.
Both are google groups users, and the Fred Bloggs troll seems to be in
a competition with A a to post the most spammy off-topic crap possible
to the group. The Gnatguy troll is just a bothersome fool. The group
would be better off all around if all three were removed.