Need Help Processing with Image J

[Emily Siska]

Hello,

I have SEM images of rubber fragments that I would like to process with Image J and I have been having a few problems. The rubber pieces do not have much contrast with the carbon tab that they are on and they are also not smooth - so there are lighter and darker spots of a paretic.  When using Image J I adjust the threshold until the particles and background have a high contrast. I try to count and find the perimeter and area of the parcels but the program seems to pick up random shapes on some particles instead of the whole thing. A friend said that its because although I see the particle as just white, the program is picking up differences and treating them like small individual particles. Is there any way around this?


Thank you for all your help.

~Emily Siska
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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Emily Siska]

---------- Forwarded message ----------
From: *Emily Siska* <[hidden email]>
Date: Tuesday, December 13, 2016
Subject: Need Help Processing with Image J
To: "Cammer, Michael" <[hidden email]>


Sorry for not attaching an example. Here are two examples. I also shared
them in dropbox.

On Tue, Dec 13, 2016 at 1:28 PM, Cammer, Michael <[hidden email]
<javascript:_e(%7B%7D,'cvml','[hidden email]');>> wrote:

> Post an example image to a fileserver and let people know so they can look
> at it.
>
> =========================================================================
>  Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical
> Center
>          Cell:  914-309-3270     Office: Skirball 2nd Floor main office,
> back right
>             http://ocs.med.nyu.edu/microscopy &
> http://microscopynotes.com/
>
>
> -----Original Message-----
> From: Emily Siska [mailto:[hidden email]
> <javascript:_e(%7B%7D,'cvml','[hidden email]');>]
> Sent: Tuesday, December 13, 2016 1:56 PM
> To: [hidden email]
> <javascript:_e(%7B%7D,'cvml','[hidden email]');>
> Subject: Need Help Processing with Image J
>
> Hello,
>
> I have SEM images of rubber fragments that I would like to process with
> Image J and I have been having a few problems. The rubber pieces do not
> have much contrast with the carbon tab that they are on and they are also
> not smooth - so there are lighter and darker spots of a paretic.  When
> using Image J I adjust the threshold until the particles and background
> have a high contrast. I try to count and find the perimeter and area of the
> parcels but the program seems to pick up random shapes on some particles
> instead of the whole thing. A friend said that its because although I see
> the particle as just white, the program is picking up differences and
> treating them like small individual particles. Is there any way around this?
>
>
> Thank you for all your help.
>
> ~Emily Siska
> --
> ImageJ mailing list: https://urldefense.proofpoint.
> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DgIFAg&c
> =j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAy
> dlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=Cs4cfj8w1NZN6KiJ7T71t
> MDKBkBQbuoEbboM_llGGWk&s=lFsqWcTt7A6H24TpIMwXRsWC3C_YVklPgu1BgxK6nPc&e=
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>
>

--
Emily Siska

Chemistry Graduate Assistant
Chemistry/HiPSEC

Science and Engineering Building, Room 2173
University of Nevada, Las Vegas
4505 S. Maryland Pkwy.
Las Vegas, NV 89154-4003
Office: [phone]
Cell: [phone]



--
Emily Siska

Chemistry Graduate Assistant
Chemistry/HiPSEC

Science and Engineering Building, Room 2173
University of Nevada, Las Vegas
4505 S. Maryland Pkwy.
Las Vegas, NV 89154-4003
Office: [phone]
Cell: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Krs5]

Dear Emily,

The macro code below might work for your images.

run("Set Measurements...", "area perimeter redirect=None decimal=0");
run("Median...", "radius=2");
setAutoThreshold("Huang dark");
//run("Threshold...");
setAutoThreshold("Li dark");
setThreshold(129, 255);
setOption("BlackBackground", false);
run("Convert to Mask");
run("Fill Holes");
run("Analyze Particles...", "size=100-10000 display add");

If too many small particles are still selected you can increase the value 100 in the last line of code. The data bar at the bottom is excluded using the 10000 in this same line.

 Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Emily Siska
Sent: 13 December 2016 23:51
To: [hidden email]
Subject: Fwd: Need Help Processing with Image J

---------- Forwarded message ----------
From: *Emily Siska* <[hidden email]>
Date: Tuesday, December 13, 2016
Subject: Need Help Processing with Image J
To: "Cammer, Michael" <[hidden email]>


Sorry for not attaching an example. Here are two examples. I also shared them in dropbox.

On Tue, Dec 13, 2016 at 1:28 PM, Cammer, Michael <[hidden email] <javascript:_e(%7B%7D,'cvml','[hidden email]');>> wrote:

> Post an example image to a fileserver and let people know so they can
> look at it.
>
> ======================================================================
> ===  Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone
> Medical Center
>          Cell:  914-309-3270     Office: Skirball 2nd Floor main office,
> back right
>             http://ocs.med.nyu.edu/microscopy &
> http://microscopynotes.com/
>
>
> -----Original Message-----
> From: Emily Siska [mailto:[hidden email]
> <javascript:_e(%7B%7D,'cvml','[hidden email]');>]
> Sent: Tuesday, December 13, 2016 1:56 PM
> To: [hidden email]
> <javascript:_e(%7B%7D,'cvml','[hidden email]');>
> Subject: Need Help Processing with Image J
>
> Hello,
>
> I have SEM images of rubber fragments that I would like to process
> with Image J and I have been having a few problems. The rubber pieces
> do not have much contrast with the carbon tab that they are on and
> they are also not smooth - so there are lighter and darker spots of a
> paretic.  When using Image J I adjust the threshold until the
> particles and background have a high contrast. I try to count and find
> the perimeter and area of the parcels but the program seems to pick up
> random shapes on some particles instead of the whole thing. A friend
> said that its because although I see the particle as just white, the
> program is picking up differences and treating them like small individual particles. Is there any way around this?
>
>
> Thank you for all your help.
>
> ~Emily Siska
> --
> ImageJ mailing list: https://urldefense.proofpoint.
> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DgIFAg&c
> =j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAy
> dlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=Cs4cfj8w1NZN6KiJ7T71t
> MDKBkBQbuoEbboM_llGGWk&s=lFsqWcTt7A6H24TpIMwXRsWC3C_YVklPgu1BgxK6nPc&e
> =
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of
> the intended recipient(s) and may contain information that is
> proprietary, confidential, and exempt from disclosure under applicable
> law. Any unauthorized review, use, disclosure, or distribution is
> prohibited. If you have received this email in error please notify the
> sender by return email and delete the original message. Please note,
> the recipient should check this email and any attachments for the
> presence of viruses. The organization accepts no liability for any
> damage caused by any virus transmitted by this email.
> =================================
>
>

--
Emily Siska

Chemistry Graduate Assistant
Chemistry/HiPSEC

Science and Engineering Building, Room 2173 University of Nevada, Las Vegas
4505 S. Maryland Pkwy.
Las Vegas, NV 89154-4003
Office: [phone]
Cell: [phone]



--
Emily Siska

Chemistry Graduate Assistant
Chemistry/HiPSEC

Science and Engineering Building, Room 2173 University of Nevada, Las Vegas
4505 S. Maryland Pkwy.
Las Vegas, NV 89154-4003
Office: [phone]
Cell: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html