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Cell Imaging - Science method

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Hi! I am trying to prepare hydroxyapatite scaffold samples for SEM imaging of cell growth. I have the Karnovsky's fixative kit but the procedure provided in the tech sheet (attached) is not sufficient for my applications. First, does anyone have a standard protocol for this SEM fixation using Karnovsky's fixative kit? Second, do I need to do the post-fix using OsO4 or is there an alternative method to the post-fix mentioned in the tech sheet? Can I do the fixation procedure without it, followed by the graded ethanol dehydration or will it have a negative impact on my sample preparation?
I would really appreciate any help answering this question. Thanks!
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If you have a cells monolayer, 30 min is a good time. If you have something like a tissue developing, with a lot of collagen, then you need 1 hr. HA is soluble in water (very slow, but still...). So if you culture started generate small centers of mineralization, you do not want to keep it too long (days, weeks) in water solutions. From the other side prolonged storage in desiccator can lead to fungus growth. Some desiccators are badly infested with fungus and need through cleaning and disinfection. From my opinion the best way to store specimens is when their preparation is complete, i.e. they are dehydrated and coated with conductive coating.
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Hello,
I'm newly working with MDA-MB 231 cells. I have sub-cultured cells using 4. 0 mL L-15 media with 10% FBS in a T-25 culture flask. The cells have incubated them incubator at 37°C, with (0 % CO2, recommended company for L-15 media). After the 48 incubations, I checked the cells under the microscope, and the cells were dead. I checked the flask also, and some of the white precipitated parts were attached to the flask. For reference, I have attached the cells Images. This is the 4th time I face this issue and I cannot figure out why. I would appreciate any suggestions/tips on what I might be doing wrong. Thanks in advance!
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hi,
the white layer on the flask is debris of dying cells. Are you sure, that the flasks are Tissue culture grade/ coated for adhesion cell culture? For me it looks like an attachment issue and all non-suspension cells die fast in the wrong type of bolltes
Sven
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We have Zoe cell imager from Bio-Rad that we are mostly happy with, but most of the time it refuses to save files to USB sticks unless they are completely empty (complaining that they are full even if they're not). As long as all files are exported in one go it works fine, but adding an extra file in a second export doesn't work.
We have been in contact with Bio-Rad, and they claim nothing is wrong with it, so now I'm just curious if anyone else is having this problem with the Zoe?
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I also have a Zoe imager and I am also experiencing this issue. Renaming the directory or burying the default export folder doesn't address the issue. Bio-Rad technical support notes that other people have reported this issue, and I am working with them to try and troubleshoot the issue.
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I have been trying to take images of my cells using 40X lens. I focus my cells first with the 4X then 20X lenses; but whenever I switch to the 40X I can't see the cells, not even out of focus. All I see is blurred image of the plate. I tried zooming in till the lens almost touched the plate but to no use.
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Dear Ayman
Check that the condenser iris aperture is set to the objective numeric aperture of 40x. In another case, I suggest checking that you are using the proper technique. Check if using phase contrast or DIC is no longer suitable for visualizing your cells.
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Hi,
Firstly, I want to say Thank You All to see my questions
I have a fundamental questions to see Fl imaging after DNA transfection.
I did DNA transfection into Neuro2A cell on 6-well. when i see FL image of each cell, FL signal of control seems whole cell body because it is just iRFP protein and FL signal of Target cells seems it is related specific subcellular organelle. (only some spots in the cell)
Before that, I wanted to check transfection efficiency and this is my experimental design.
i) Trasfect cell with DNA plasmid on 6-well (control and target dna plasmid each)
ii) after 1 day, transfer cells on slide glass for confocal imaging
iii) DAPI staining and check (# of transfected cell/# of whole cell) x 100 to check the efficiency
and the questions are
i) do i need to fix the cell to see confocal imaging?
ii) is it okay transfer cell from 6-well to cover glass after cell transfection
If there is better protocol or opinion, Please tell me, it would be very thankful.
Thank You,
Jeongwon Park
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Hi usually we do imaging a day after the transfection because sometimes after the transfection if you leave it for 3 days. The non transfected cells can over grown on top of the transfected cells which would then be on your way. So ideally we do imaging the day after transfection.
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Does anyone know a simply way (i.e. using free image softwares) to quantify chromatin condensation? Cells were labeled with DAPI and analyzed by confocal microscopy.  
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You can calculate the chromatin condensation parameter (CCP) simply by staining the cells with DAPI.
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I am using Matlab for image segmentation watershed algorithm has been done successfully , i want to ask how do i further segment each cell image and segment each blood cells and label them in different article i need Matlab complete code
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Dear
Kalyan Acharjya
i want to detect and segment each blood cell from the blood cell image using neculie segmentation but i want to use SBF and Laplacian Gauss Algorithm
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I have been using Fluo-8AM for imaging calcium transients in ATDC5 cells following drug administration. I have had no problem using it in prior experiments and even the first samples with a newly generated stable cell line. Recently, following staining/incubation/washing, my cells no longer keep their normal morphology and begin to ball up , increase their spontaneous signaling, and eventually become unresponsive to the drug I use to induce signaling.
I've tested incubation and media temperature, the use of pluronic f-127 in the calcium staining media, and different dishes (96, 24, and 6-well [MatTek] all glass bottom, some TC some not). The cells are healthy before the staining but the staining process now seems to 'kill' them. I'm quite careful during the handling of the cells during media removal/washing, so I'm not sure if the dye is causing any issues.
Has anyone experienced this issue before? Thanks for any help.
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Optimizing the loading of AM dyes on the microscope stage is an excellent suggestion, as cell types show tremendous variability. Loading times tend to be in the 10-30 minute range. At temperatures approaching 37C, AM dyes can selectively load into organelles like the ER and mitochondria causing damage and/or non-cytosolic Ca2+ signals. You can use the microscope to check the dye distribution, a dark nucleus would indicate some ER loading for example. After a wash, you can also check to see if your cell type actively pumps out the dye, if so you may need to include something like sulfinpyrazone.
Make sure the DMSO used is OK.
Keep the dye around 1uM - loading is dependent on esterase activity, so higher conc. doesn't help.
Add pluronic to ~10% volumes of dish media, then add Fluo-AM to that, then add all to dish
You don't need to worry about -AM dyes binding Ca2+. The acetoxymethyl (AM) groups prevent that. Even if the dyes did bind Ca2+, then the effect would only be in the low micromolar range while extracellular Ca2+ is ~1000fold above that at 1-2mM.
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I need some suggestions about differentiation process of U-937 cell line. It would be about seeding concentration of cell, PMA concentration for treatment or resting step ...
If you have, could you send to me cell image for each step...
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Hi Adem,
You can differentiate U-937 cell line using "a differentiatial mark" that we had utilized in our experiments with PMA-stimulated U937 macrophageal cell line. Namely, as U937 cells respond to the presence of LPS with a marked increase in the rate of cellular AA metabolism and cytokine release into the extracellular space, we measured activity of cyclooxygenase 2 (COX), which catalyze the key step in the conversion of cellular arachidonic acid into prostaglandins. The COX-2 expression is strictly coordinated with up-regulated in PMA-differentiated U937 cells stimulated with lipopolysaccharide (LPS). At the same time, COX-1 is not up-regulated at all. In turn, another "market sign" we'd used from time to time was enzymic activity of the Mg+2-dependent phosphatidic acid phosphohydrolase 1 (PAP-1), because up-regulation of COX-2 strictly depends on the PAP-1.
In regard to your request on seeding concentration of cell, PMA concentration for treatment, and on phenotypic and morphologic changes observed in U937 cells after treatment with PMA (100 nM) in the presence of Haemophilus influenzae, please read this paper of Dr. Jahn and colleagues 
Best wishes,
Ilya
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I usually use PFA 4%. However I must fix cells (Hs 578Bst) with a not hazard-toxic compound. I thought to use air flow comes of biological cape, but the morphology must be affected. Some suggestions are more than welcome.
Thanks to everybody.
Luca  
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Hi Mohammad, tank for appreciating our past discussion. As far as cel fixed are concerned, I've mostly used PFA4%. It is the one of the best chemicals, used for cell fixation, recommended for AFM. I suggest you to scanned the cell at least 24 hour later cell fixation, unless the protocol required differently. AFM preserves cells from any kinds of changes made by time. I scanned cell samples fixated 8 years beforehand. Concerning the essication, made by biological cabinet airflow (30 minutes, no more), it depends what you want to look for. In my latest AFM experiments I fixed cells by airflow, and the samples were perfect. I would like to suggest to consider also the airflow fixation, not for long time or you must seriously shrink samples. I hope my reply will be helpful. :-)
Cheers
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I want to analysis bio availability and integration of liposomal drug in cancer cells. How the cell line sample was prepared for raman analysis to obtain single cell images and respective spectrum? And how the VCA or MCA was done?
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You might want to take a look at the attached paper. The principle and implementation of VCA and other techniques were mentioned.
The cell line was prepared as described in Section 2.1.
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Hello!
Has anyone used MitoSOX™ Red mitochondrial superoxide indicator *for live-cell imaging* (M36008) for suspension cells? I want to analyze fluorescence with a plate reader. I am wondering whether washing step in the protocol wont affect my cells - for adherent cells is not a problem but suspension cells must be centrifuged and I don't know how to make it without affecting cells. Does anyone has experience with this analysis with suspension cells? I will be grateful for some tips!
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Hi Agata,
I was wondering if you got/have a MitoSOX Red protocol for suspension cells.
Thank you.
KJ
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Hello,
I have problems to set up the experimental conditions to see endosome maturation in Hela cells expressing GFP-Rab5 and Cherry-Rab7. I am using ZEISS LSM 880 with Airyscan for Life Cell Imaging, with objective 63X/1.4 oil. There are many publications with the method published but I still don't manage. My main problems are:
- To many endosomes that move extremely fast. I cannot track the endosomes as they disappear in the Z position or they mix with other endosomes making it difficult to differentiate the ones being tracked. I tried to do Z-stacks but the focus is lost.
- Some bleaching of the cherry tag as I acquire pictures as fast as possible (every 5 sec) because the endosomes move very fast.
- Cells move so the focus is lost with the time as well.
Has somebody conducted a similar experiment? Which microscope have you used? Can you advice how to improve the experimental setting? Alternative mammalian cell line that I could use (easy to do a KO and easy to transfect/transduce)?
Thank you and kind regards,
A.
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Hi,
I am currently facing a similar issue. I believe Spinning disk confocal microscopy can help imaging (especially if you need a Z stack) at faster rates, but I have not tried that myself. Have you been able to find something that helps? I do not want to image my cells at 4 degrees as that affects the uptake of my compound by the endocytic pathway, so I am trying to find techniques with better resolution (unsuccessfully).
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Hi
We recently bought Nikon eclipse Ti2 inverted fluorescent microscope.
It claims that it can get very high-quality images. In bright field it is OK (not superb!) but when switches in phase contrast, the quality of images are not good at all. The technician from Nikon just introduced the image processing capability of the system.
The instruction of the device is also full of explaining unnecessary data and is not user-friendly. Does anyone have any suggestion to get better quality images using this system?
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Well, if the microscope is not damaged then the most likely culprit is that it is not calibrated correctly. Have you gone through the entire process of aligning the optical path? Are your phase plate and annulus properly matched? Is your Kohler illumination aligned? Are your samples sitting flat on the stage? Is your camera in the correct alignment in the optical port?
The microscope itself is professional grade. You should be able to take clear images in any mode so long as it is in working order.
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I am taking photos of cells in culture using a FLoid™ Cell Imaging Station. I would like to add a scale bar on ImageJ. I know I need to go to Analyse->set scale, and input the information regarding pixel size in microns. I know the image resolution is 1296 x 964 pixels. But I am unsure of how many microns are per pixel. What am I missing?
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Glad it worked.
I would recommend taking an image of anything with each of the objectives and at each bin setting using your system. Then embed the Scale bar using the FLiod software as you did and measure the length in ImageJ. Then just make a table of the conversion factor between pixels and microns for each objective and binning for future reference.
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Hello everyone,
I hope you are doing well.
Is there any free soft that I can measure the distance between cells on the time lapse cell image? I have time lapse images of dissemination of cells from cell body. I want to measure how many cells or how far they move from the cell spheroids compare to the control. I am thinking of checking the images (interval would be 10 or 20 min) and track the cells from spheroid. is there any free program that I can do it, let me know please. Thanks in advance
Have a nice weekend.
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Sounds like something that could easily be done with ImageJ. I like the FIJI distro.
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Hi,
I would like to know would it be possible to measure the colocalisation between 2 dyes / stains in the IHC stained tissue using ImageJ colocalisation algorithm. I notice that the image J colocaliation algorithm  only used for fluorescence stained tissue. We have another option to use colocalisation algorithm by aperio, but it costs a lot. 
KIndly advise me for any software that able to measure dual color / colocalisation in IHC stained tissues.
I truely appreciate all the replies and suggestions.
Thank you.
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If I understand correctly, you are trying to analyse co-localisation in an enzymatically stained sample? So the problem is that you can't distinguish the 2 separate stainings in separate channels? In that case I believe you can try to use an ImageJ colour deconvolution plugin, such as is available in FIJI. After that, if the deconvolution was successful (it might need optimisation), you might be able to do colocalisation analyses. I hope that helps.
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I am planning for an experiment using MitoTracker. I wish to do time lapse study in vitro. I want to know about the stability of the mitotracker dyes. For how long is the fluorescent intensity maintained? Is it possible to add the dye, then perform the experiment and then visualize the cells. The experiment will last approximately 48 hours. If not, can you suggest some alternative for the same?
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I don t know for mitoTracker, but if the dye is not stable enough for a 48h video, you can try to transfect/infect your cells with mtDsRed plasmid/virus. the fluorescence might bleach at some point so you should try to acquire at a low frequency. For that, you need to be sure that this frequency is appropriate for analysing the biological process (velocity, morphology, fusion/fission) you want to study.
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I usually use blue DAPI to visualize nuclei, but I have seen articles where they report nuclei with a DAPI staining in purple but they do not report the brand or the catalog number and I have not found it. I think it is due to a combination of red and blue channels, someone could guide me
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Yes, looking at the figure, it is clear for me that authors used purple instead of blue to show DAPI.
It is common now to see such color in publications. Blue may be difficult to see on dark background and purple is also used for the colorblind people.
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anybody knows how I can get propidiom iodide stainining image by olympus BX53. I couldn't find defined channel for PI?
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Try to use the red channel/filter (eg. Texas Red) if it is available on the microscope. 
 Fluorescence Image Acquisition for BX53
1.Click the FL button on the remote controller box to use mercury arc lamp light for fluorescence.  The light can be on or off by pressing FL Shutter button on the remote box.   
2.Select an appropriate fluorescence mirror cube by pressing Mirror buttons in the controller box or clicking any one of the Observation Methods buttons   (except BF and DIC). The selected mirror will be in position 1.  Make sure that the light path bars are in correct position (the upper bar at the mid or extended position and the lower bar pushed in) and camera is selected.  
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In SEM, I heard that "The optimum condition for imaging is when the escape volume of the signal concerned equals to the pixel size", what dose that mean?
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The cited statement is right only in pure theory.
In practice it means that beam intensity (called "spot size" by some manufacturers) should be changed with magnification - higher intensity for lower magnifications. In this way operator can achieve right balance between image sharpness and noise level.
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I need to isolate diatoms from the various other debris, wat are the possible methods? by using inverted microscope, How can we do ?
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Thankyou, but will glass pasteur pipette be visible under the objective lens? what is the minimum objective lens required for that? 40x or 400x ?
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I wonder if someone used the imageJ to analyze the puncta-like fluorescence intensity using Image J software? I tried to quantify the intensity using regular method, but the S.D. appear too high, the regular CTCF (corrected total cell fluorescence) method might not be proper for the puncta-like staining. Who knows how to quantify it? the picture i attached is the one i hope to quantify. Thank you.
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Dear Mou. The columns you use to set a calibration, for example: if what is black in the image represents 0 mg of calcium (just an e.g.), and the strongest red is 25 mg of calcium. In this case, you can make a calibration (in this case using only 2 points, the zero and 25... ). So, as black is represented in ImageJ (8 bits images) by zero, and white (red in the case you choose it in the lookup table) is 255.. so you can make
in the left column:
0
255
in the right column:
0
25
and choose the straight line for the function. 
After calibrated, you can select an ROI (region of interest) by choosing the forms (rectangle, circle, etc.) available, and then go to Analyze>measure (CTRL+M) and you will have a statistics of the region you selected.  You can also go to SET Measurements to select what do you want to measure...
Hope it is what you are looking for...
All the best
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I'd like to image ROS accumulation in cells with a fluo dye and I'm wondering if anyone have ever performed cell lysis to mesure ATP after ROS imaging ? Does the ATP quantitation is still reliable ?
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Hi Guillaume,
Unfortunately, it's practically unreliable assessing the ATP quantification in the cell lysates in which ROS accumulation was undertaken. Just compare the toughness of the later procedure, in order to imagine the inability of coexistence for delicate ATP reaction.
Intracellular ROS levels usually assess using the CM-H2DCFDA probe. Cells grown in 96-well flat clear bottom black polystyrene microplates are washed twice with 150 μL of HBSS to remove culture medium. Then, 50 μL of the probe (7.21 μM in HBSS) added to each well and the plates are incubated for 30 minutes at 37°C. Excess probe was discarded and 100 μL of the prooxidant solutions prepared in HBSS added. After the incubation, cells are lysed by adding 50 μL of 0.5% Triton X-100 in PBS. Cellular levels of ROS are visualized under the microscope using CM-H2DCFDA fluorescence live cell imaging; cell fluorescence images captured using an epifluorescence microscope.
At the same time, intracellular ATP determination performed by a bioluminescence assay based on the ATP-dependent luciferin-luciferase reaction. A new internal calibration standard of ATP usually prepared each day in a range from 1 to 100 μg ATP/mL prior to readings. To determine the cellular ATP content, cells grown on 96-well white clear-bottom plates were first incubated for 3 minutes with 25 μL somatic cell ATP releasing reagent and then for 3 minutes with 25 μL of sterile water. The plates placed in a Luminoskan RS luminometer and 50 μL of the luciferase-containing buffer (adenosine 5′-triphosphate assay mix) added to each well just before measurement of the light emitted, which is proportional to the ATP concentration. 
Best wishes,
Ilya
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a) Leica DM4B
b) Zeiss Axioimager 2
c) Nicon Eclipse NiE
d) Olympus BX53
How config is the best performance for FISH staining of chromosome?
Could you give me a detailed config of fluorescence microscope or filter?
Which one can I prefer?
Thanks a lot from now..
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Thanks so much for all infos
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I am using gfp tagged chloramphenicol marked staph aureus and normal gfp tagged pseudomonas for my antibiotic studies. I find that there are few rod shaped bacterias in the staph aureus cultures while doing confocal imaging. Can the appearance of rod shape give rise to changes in shape of staph aureus? Or could there be a contamination of pseudomonas? Or what are the chances of e.coli engulfing staph aureus and glows green?
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Thank you Dr. Rad for sharing the article. Appreciate your help!
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How to measure fluorescence intensity of cell membrane vs cytoplam stain of a 2 ch. confocal img where one is cell mem. and other ch is a antibody.
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Hi Md. Amran,
To practically solve your issue (that requires an accurate cell segmentation by image processing), I suggest that you follow these links:
  1. Measuring Cell Fluorescence using ImageJ”, 2011 on ScienceTechBlog ( https://sciencetechblog.com/2011/05/24/measuring-cell-fluorescence-using-imagej/ )
  2. Carpenter et al., “Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for CellBased Screening“, 2009 ( https://personal.broadinstitute.org/anne/publications/40-Ljosa_PLoS_CompBiol_2009.pdf ) including an exhaustive enumeration of available commercial & open-source image analysis softwares
  3. Linblad et al., “Image Analysis for Automatic Segmentation of Cytoplasms and Classification of Rac1 Activation”, 2003 ( https://pdfs.semanticscholar.org/2b94/b4a20771f4ca9c9093e39a0e22922d4953a9.pdf )
Here is an excerpt from (1) Carpenter et al, 2009: “…It is sometimes unnecessary to precisely identify the cell boundaries: for instance, to determine whether a protein is predominantly in the nucleus or the cytoplasm, it can be sufficient to measure the average intensity of a protein in the nucleus and in a ringshaped region around the nucleus, as a proxy for the cytoplasm…
Note: this computational technique may be extended to calculate fluorescence intensities within 3D cell structures via ImageJ plug-in “WatershedCounting3D” ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607619/pdf/cl-2-176.pdf ).
Here are some complementary references of interest:
Finally, in addition to the here-above valuable reference suggested by Hermance Beaud ( https://blogs.qub.ac.uk/ccbg/files/2014/05/2014-05_Analyzing_fluorescence_microscopy_images.pdf ), some readings about the –comparative- use of ImageJ and Fiji: 
Hoping it will be helpfull
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Hello, I am currently working with human Jurkat T cells, fixing in solution and then acquiring images with a super resolution microscopy that we work with but I found that if I fix cells with PFA 2% cells have lots of autofluorescence, in all wavelength. I cannot found in the bibliography of immunofluorescence techniques using this cells any case, anyone had similar results? 
I attached a picture of one cells, illuminated with 647 20% of the laser power. 
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We use a super resolution microscopy (STORM) which is more sensitive to fluorescence that a normal fluorescence microscope. With the polymer, which is label with Rhodamine, I can see exactly the same profile. In fact at first I thought that I did a mistake with the negative control and it was not the real sample. 
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performed dot blot hybridization using DIG labelling but no result even in positive control.
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Short answer, your experiment failed.  Have the reagents you used given positive results before?  Were your samples and reagents fresh?  Have you done a successful dot blot before or is this a new technique for you?  You are going to have to give more details to get specific help.
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Mitochondria have been stained using mitotracker dye under different experimental conditions. Is it possible to use software or an imageJ plugin to quantify mitochondria? The mitochondria cannot be easily counted by hand given the resolution of the microscope.
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Your best bet is to just do total fluorescence intensity in the mitotracker channel. It's always difficult to count mitochondria by a total mitochondrial stain partially because they can span imaging planes fairly easily.
If you wanted discrete counts, best to use something like a mitochondrial DNA stain that should only correspond to one spot per mitochondrion.
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I have taken Z-stacks and timelapse for two fluorophores in HeLa cells. I have the full hyperstack. Can anyone inform me, how to assemble it for a video file?
Thanks in advance,
Arka Ghosh
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Split and segregate the z-stacks for each time point. Then take each of the z-stacks and go to Iamge - Z porject - maximum intensity. You will get a maximum intensity projection for each of your time point from the z-stacks. in this way. Now go to Image - Stack - Images to Stack. You will get a stack with all the max. projections from each z-stack as a time series.Hope it works for u.
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Does anyone have recommendations for breathable plate seals for 96 well plates that are compatible with fluorescent (high content) imaging, in other words are not autofluorescent/ increase light scatter in the well?
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I am planning to label dextran with Texas Red and then study the uptake by different cell types. 
Anyone have any idea how to conjugate Texas red to dextran and then any clear protocol to study the uptake by using both plate reader(measuring protein) and confocal microscope?....
Thanks 
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Dear Attila, thank you, I will buy labelled one. Do you have a clear protocol for studying the uptake by labelled dextran?
Thanks
Alaa
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I'm now needing to image cell cultures. I am thinking about transiently transfecting a fluorescent DNA marker, but I think it will be too sparsely labeled for my purposes. And throwing a dye on would be simpler and would let me know if more rigorous methods were called for.
Does anyone have a reccomendation for good live nuclear staining dyes?
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There are many nuclear stains but the two best dye versions (and easiest, no transfections required) are Hoechst  and SIR-DNA (from Cytoskeleton).  Both are bright dyes that when used at the appropriate dose (I use 1ug/ml for Hoechst and 250nM for SIR-DNA) you can timelapse image for 24 hours or more without significant photobleaching.  Neither dye (at low doses) inhibits cell division or cell migration. Both are great for cell tracking. Hoechst excites in the 365nm  range while SIR-DNA excites with 642nm.
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Hello everyone,
analyzing the histology of ventricles includes measurement of the ventricle diameter in histological images. Thus I am looking for a method or plugin for either ImageJ or Image-Pro Plus to do so.
There is Fischer's vessel diameter plugin for ImageJ(https://imagej.nih.gov/ij/plugins/diameter/index.html) but it depends on a single line selection.
The diameter measurement of Image-Pro Plus measures the Diameters of objects within the polygon selected area of interest. Both systems offer no solution for my problem.
My idea of how it could work is that the software measures the average length of diameters measured at 2° intervals passing through the centroid of the polygon after drawing a line around the ventricle using the polygon selection tool (implemented in both Imagej and Image-Pro).
Does anyone know such a system or a similar solution?
Any answer or comment is highly appreciated.
Thanks in advance!
C. Halim
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Dear John and Hesham,
thank you very much for your comments.
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I have YFP tagged STIM1, transfected in HEK293 cells and imaged in TIRF plane for formation of punctae/clusters upon ER store depletion with thapsigargin. I have been trying to analyze the number of clusters and area, intensity of each cluster using ImageJ. 
However, I have uneven illumination and background in the fluorescent images in TIRF plane. And, the clusters are of different sizes. So, I am facing difficulty to subtract background and set a common threshold for both small and big clusters. I tried FFT filter, background correction, local threshold but nothing helped so far.
Has anyone analyzed such clusters? Any help is much appreciated.
PS: I have attached a sample image with clusters.
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Try the rolling ball background subtraction in ImageJ.  It does wonders for unevenly illuminated fields.
The better solution is to use a Chroma slide to check that your beam is centered.  TIRF uses single mode fiber with a Gaussian beam profile, so it will always be brighter in the center and fall of at the edges.  Put the cells in the center of the field. 
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I'm looking for a dataset of images (>100 images) of cells under bright field microscopy. They can be from any species, but human or mice cells are preferable. I have found a couple of sources such as the cell image library but it does not seem to contain bright field images in the quantities I need.
Also note, I am looking for images of cell cultures in particular where only one type of cell is in the image. As such images of tissue are not suitable for my application. 
The reason I am looking for these image is to test some image recognition and classification software. 
Thanks in advance. 
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In the following paper by ZaritskyEmail et al., "Benchmark for multi-cellular segmentation of bright field microscopy images" BMC Bioinformatics201314:319 DOI: 10.1186/1471-2105-14-319, they talk about a dataset of 171 manually segmented images of 5 different cell lines at diverse confluence levels, acquired in several laboratories under different imaging conditions in the first figure.  HTH.
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the bacillus spore was viewed under microscope and I got difference morphology of the spore.
the first picture is pure spore suspension stained with malachite green 0.5%.
2nd picture is transparent cell looks like spore
3rd picture is a group of green color unknown particle.
may i know are they all spore? 
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Currently with cellSens Standard version1.15 and below,.vsi file can be opened with ImageJ Olympus plugin, but not for version 1.16. Would like to know if there is a compatibility issue which can be the one causing this problem.
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Dear Celine Choo
You can join this ImageJ Forum, we discussed alot of issues about imageJ in relation to Image-Pro Plus and you will find your answers.
This ImageJ Forum for those interested in morphometry. the link is provided:
Are there any plugins for Imagej or a method for Image-Pro Plus to measure the mean/average diameter of polygons?. Available from: https://www.researchgate.net/post/Are_there_any_plugins_for_Imagej_or_a_method_for_Image-Pro_Plus_to_measure_the_mean_average_diameter_of_polygons [accessed Apr 15, 2017].
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I am trying to use JC-1 to stain the oocyte, however when I put the oocyte on the slides and cover the coverslip, the oocyte will be destroyed. I am the frist one doing this in my lab, so did anyone provide the correct way doing oocyte confocal? That will help me a lot.
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Thanks, Michaela and Usama, It helps a lot, I'll try to use the vaseline frist, if it doesn't work well, I'll buy the Fluro-dish. Thank very much.
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I am trying to analyse RNA synthesis and obtain pulse-chase upon silencing of my GOI. I would like to obtain RNA content from the cells under different time courses which will be measured via FACS and Immunofluorescence simultaneously.
Any suggestions will be highly appreciated. Thanks in advance.
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Thank you so much. Indeed, knowledgeable information. I am quite familiar with Brd-U labeling of different cells including cardiomyocytes of my interest. I am seeking BrU labeling to analysee RNA stability via pulse-chase.. which can be alternative of usage of intercalator like actinomycin D.... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583853/pdf/rna-9-1233.pdf
Thanks again.
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We had cultured, fixed, and stained cells directly in the wells of a standard 6-well tissue culture plate. However, we are realizing we need to do higher magnification to see some of the staining features, and because our confocal is inverted it would be best to punch out the wells or cut them out in some way so they can be mounted under a coverslip and imaged. Does anyone have a suggestion for ways to do this?
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Hi Justing:
No sure if you are aware or not, but they are commercially available (albeit overpriced!) https://www.mattek.com/store-category/cultureware/glass-bottom-multi-well-plates/.
A cheap alternative we have done in the past, is to simply heat up a cork borer (i.e. the metal tool for cutting a hole in a cork or rubber stopper) of the desired diameter and simply punch/melt a hole through the bottom of plate/well. Don't get the metal too hot or you will end up melting away a larger hole; with the right temperature you will get enough heat into the borer to help it move through the plastic smoothly.
Then just glue a round coverslip to the bottom (outside face) of the plate using sylgard 184 or your favorite adhesive. Works great for plating and imaging or as a recording chamber for patch clamp experiments. 
Hope this helps. Good luck
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I am working on a project in which I need to count cells stained with Cy3 and Prodynorphin. I am trying to find the best way to automatically count the double-stained cells. Currently, I am using ImageJ to threshold everything within the desired color range and then removing the other colors. However, I think this method may be unreliable, as the color range for the double-stained cells isn't very clear. Does anyone have any suggestions for a better way to do this?
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I recommend scanning slides with a ScanScope XT and analyse images with an eSlide Imager (Aperio, Vista, US). Hope this helps, Tom
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Are there any methods/assays available to detect or quantify riboflavin inside the cells without using fluorescence spectroscopy/microscopy? Since I am using cultured cells, detection in cell lysate can also be considered. 
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Is what you tried to use HPLC reversed with solvent mixture in gradient mode
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I used Hoechst dye to stain fixed cells for high content object count. I have read that MTT and resazurin induce morphological changes on NIH3T3 cells, and some papers suggest to use GF-AFC reagent instead of MTT. Could that be the reason? 
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Hi,
Please note that:
We suggest using two cytotoxicity assays instead of just one. This is because certain chemicals have been reported to give divergent results in different toxicity tests including the NRU and MTT assays (Olivier et al 1995; Chiba et al 1998). Besides, Evans et al (2001) have recently found that in some cases one of the NRU or MTT assays can be more sensitive in detecting the toxicity of non-viral transfection reagents.
Evans, A.R., Alexander, D., Burke, P. and Reed, C.J. (2001) Toxicity and transfection efficiency: comparison between four commercially available non-viral transfection reagents in a human bronchial epithelial cell line. British Pharmaceutical Conference Science Proceedings 2001,  106.
Pls also see attached research article.
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Hi,
 I was working with Mycobacterium Smegmatis. The cells cluster are not spherical in a 2D plot but appears in the form of ROCKET. I am attaching two figures for kind convenience. The figure shows control M Smegmatis cell without any fluorescence!! the pattern of the cells looks weird!! If this is because of autofluorescence then how do we find out and gate for true fluorescence in positive cells.
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Have you access to a fluorescence microscope? I would suggest that you look at single bacteria first.
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Hello.
I work with phospholipids.
It is necessary to quantify phosphatidylserine on the outer and inner surface of the membrane. How to do it? What kind of dyes used?
I know, I used annexin V with flow cytometry. I have no flow cytometry. Which method is suitable for Fluorescent microscope?
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 Dear, Babu Mia, my task is to quantify the content of phosphatidylserine in the outer layer of the membrane. I can not find a technique how to do it = (. I do not have the opportunity to do this with flow cytometry.
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Hello everyone,
I want to do SIM with three different proteins in living cells. Therefore, I need three different fluorescence proteins with high photostability and high brightness? Could anyone suggest a combination (blue, green and red)? Especially I need a good advice for choosing a blue and red FP. 
Thanks for your help and your suggestions! Best Andreas
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Find the "brightest" FPs and choose those - http://www.fpvis.org/FP.html
mNeonGreen looks good.
Modern CFPs are mTurquoise2 and/or mCerulean3, CyPet or mVenus for yellow. mCardinal or mSmurFP maybe for red
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Is there any way to visualize a fluorescent drug loaded inside the nanoparticles? I think confocal microscopy won't help due to the small size of the nanoparticles and TEM won't be useful too.
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You could try fluorescence imaging. Check for fluorescence emission from the drugs loaded in nanoparticles if the nanoparticles are non-fluorescent. In the absence of fluorescence from nanoparticles, the fluorescence has to come from the drug present in the nanoparticles.
But there are other methods such as infrared spectroscopy. You could identify unique characteristic IR bands of the drug molecule and check their presence in the sample confirming the presence of drug inside the nanoparticle.
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Hi!
We want to do super resolution microscopy of stromal vascular cells isolated from adipose tissue.
As these cells are extremely sensitive, we can't culture them on glass microscopic slides (which would be ideal for high resolution microscopy, due to its minimal auto-fluorescence).
Does anyone know a coating procedure for glass slides that would suit cells of the stromal vascular fraction?
Or plastic microscopy slides with a thickness lower than 0.17mm?
Thank you!
Best,
Karin
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Thanks
We are planning to do high Resolution Imaging (STORM) and confocal Imaging. So normal analyzers like JuLI are no option. That's why I need a thin microscope slide that suits very sensitive cells and high Resolution imaging.
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I found a lot of fluorescence pictures of primary cilium stained with alpha-tubulin antibody in the literature, but I am not sure if they made by confocal or epifluorescence microscope? Will I see it in epifluorescence mic. or do I need confocal? thanks
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Hi Magdolna, I had the same before, used alpha-acetylated tubulin antibody on human airway epithelial cells grown in liquid culture and I only saw cytoskeletal structure (with the confocal). Cilia would normally appear in air/liquid interphase cultured, therefore structually differenciated cells. So if you dont see cilia on the wide-field I think the chances are good that there are no cilia. Best, Anita
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how to merge acridine orange and ethidium bromide staining pictures?
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@Srinivasa Rao Palla:  even if the specialist knows that you wanted to name the dye....
would you - please - mind to correct (using the edit-function top right edge/margin to your question-form....)   the wrong / misspelled "according" in the title of your question to "acridine orange" (this honestly asked for better searchability in RG-archives....)  Thank you! 
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I am having difficulty in observing the karyotype of Canna lilies under a compound light microscope. can anyone please suggest the right type of microscope to use in dealing with minute chromosomes? 
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Hi,
have you tried confocal microscopy?
Thanks! Good luck!
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Histologically stained slide how to choose area for selection of adipocyte?& how to mesure the size?
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Hi,
You can do it easily with the ImajeJ program. You can set an threshold for the roundness of the adipocyte size and tell the program to count every cell that have x and z size and the ones in between will also be included. The program is automated but you can add and exclude cell once you are done. It will give you the celk area, cell number and perimeter. You do need to apply and color deconvolution on your image and use the  color that will suit better for your analysis. 
Erika Barboza
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Hey everyone,
we would like to grow cells of one cell line in a way that it sticks to the top of cells of another cell line like it is depicted schematically in the attached file. The easiest way would probably be to just add cell on top of a confluent layer, but we would like to avoid that. Instead, we would like to have single cells of one line with cells of the other cell line attached mainly not to the coverslip, but to the top of the first cell line.
Does anybody have a method how to do that?
Thanks,
Leonhard
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Hello everyone,
I am trying to measure Young's modulus on plant cell walls. I am usin atomic force microscopy to do it. I tried fixing my cells with poly-l-lysine and it does attach some cells, except that cells keep moving on one side or slide whenever the cantilever is scanning them. Anyone has an idea about how to fix the whole cell file ad keeping it from moving while scanning?
Thank you
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Dear Fatima,
thank you really for detailing your trials. I imagine the problems you are facing (I have to admit:  imagine "theoretically" for AFM-examination) but as you certainly found out I was working in the "branch" of diagnostic TEM formerly and also have a wide background to SEM, AFM and other microscopical techniques as read by literature rather than personal experience).  So your approach, to include your Arabidopsis thaliana cells into liquid low-melt agarose at first glance seems interesting and promising....   the problem will be the intermediate drying and then re-wetting of the cells (in appropriate buffer..., guessing you can not fix your plant cells prior to examination because you want to find out not only morphology but also  the Young modulus in living cells). Other AFM articles / work report adhering cell material (e. g. homogenized and therefore 'hackled' prior to imaging) to mica-sheets.......    since you intend to use a cell suspension under liquid conditions for measurement I guess that literally physical "adhering" will be impossible...  the only way of keeping your cells alive for measurement in the low melting agarose film (low melting gelatine too ??) IMHO would be seeding your cell material to the moist agarose layer - stirring and cooling down until the agarose is solid...attempts to measure then would need a cooled chamber/ setting....this might be difficult and delicate circumstances....Hope there are out other ( the real )experts, wish you all the best, good luck, WM
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I am working with stromal cells that have been fixed- I am wondering if it is possible to do hoescht and nile red stains on them like I did with stromal cells in culture 
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I would say, it depends on the way, how cells have been fixed. Some fixatives destroy or alter lipid structures, which would result in disturbed lipid staining by Nile Red. If possible, I would suggest labeling with Nile Red before fixation and use a gentle fixation method, such as paraformaldehyde, 2% 10 min on ice.
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I am working with Quantum dots for some therapeutical applications. As a part of it, I am using versadoc 500 fluorescence imaging instrument for quantum dots imaging studies. As a result, I am getting emission in all the region (blue, green, yellow and red). I want to know that how to filter the particular emission for example: my quantum dots has only red fluorescence. Is there any separate filter to proceed with this or I have to made changes in settings while calibration.
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Thank you Jan,
      Ya i am getting the emission and excitation for quantum dots at a time. I dont know how to rectify this issues. I tried green LED for excitation and used the standard filter#4. Also How to get the 640BP35 filter active. There is no display of this filter. It seems, in manual they mentioned "AN OPTION 640BP35 FILTER IS AVAILABLE". please guide me, how to proceed with this instrument for selective filter emission for particular wavelength
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I understand that if you have 3 mice and are generating data from microscopy images, you might want to average the data in such a way that you enter in 3 numbers to Prism for example.
Should you handle in vitro microscopy data in the same way? For example let's say you are interested in the intensity of a fluorescently stained protein on cells. You do the experiment 3 independent times (n = 3). For each experiment you have cells seeded on 4 coverslips. For each coverslip you take images from 5 fields. Within each field you might have 10-15 cells. 
How many numbers do you ultimately report (i.e. how many numbers go into Prism). Do you put in every cell you analyze? Every coverslip? Or 3 numbers for each experiment? If you average them, should you take an average of the coverslip and then average the coverslips? Or just average all the cells in the experiment?
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Hi Joe, in my opinion this is the way it should be.
You can also do statistics within your groups, but this will only show your inter-experimental variation (technical n).
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Hi,
I am trying to quantify green (viral protein) and red (apoptotic marker) fluorescence. How do I use Image J to perform this function. FYI, my picture has multiple R/G dots/puncta. I have attached two sample images for your perusal.
Thanks.
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If you want to measure puncta specifically, it's not as simple as the above response. In that case, can use automatic threshholding (Image > thresholding on Image J toolbar) to essentially eliminate the background fluorescence, such that your image will only display the puncta. From there you can quantify the puncta. You will have to play with the thresholding a bit to get your desired result. Another possibility method is to use the "substract background function" (process > subtract background) to remove the diffuse fluorescence such that only the puncta are visible. To quantify the puncta, you can "analyze particles" (analyze > analyze particles). Otherwise, if you want to simply calculate the overall fluorescence you will first need to "set measurements" to determine what info you'd like (I suggest checking the following boxes: area, min/max gray value and mean). Then you can measure (analyze > measure). You will need to copy and paste the raw data into an Excel spreadsheet from there.
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Hi Vipin,
the accurcy of your localization is strongly depending on signal to noise, pixel size and the size of the point spread function. You might want to take a look into this publication doi:10.1038/nmeth.1447
The experimental localization accuracy is often measured as the FWHM of the distribution of a big number of localizations from one emitter. For example: localize one bead a thousand times and analyze the distribution of the thousand localizations.
Best,
Thorge
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Hello everyone,
So I have a microarray on a glass coverslip (1.5 mm thick). I would like to create incubation chambers on it so I could use one array for several incubation targets. I did some lookup and it seems like there were only those designed for microscope glass slides.
Any ideas are greatly appreciated.
Diem
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It is just idea below not an experience :)
Do incubation chamber as usual and use not microscope but cover slide for later steps.
A couple tape on microscope glass slide + drop of binding media + inverted cover slide with array.
Have a nice day!
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A431 cells observed with an Olympus BX-51, 100x magnification. 
I noticed aggregates indicated by arrows, randomly diffuse in the cytoplasm; someone is visible also in the nucleus.
I can not tell if they are aggregates or some kind of contamination.
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I have never observed such kind of inclusion body in A431 cells. In my opinion, the contamination is the most likely. How about the doubling time of the cells?
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I am analyzing 3D-reconstructed images taken of embryo vasculature. In these images, I am trying to understand the behavior of endothelial cells; comparing controls with mutants. So far I managed to have the X,Y, Z coordinates of these cells. I am trying to figure out how clumpy they are. And compare that between controls and mutants. 
So basically I am trying to analyze the data using these coordinates. I am sure that there some sort of formula or plot that can show me how clumped these cells are. 
I am wondering if anyone has a good background with this.
Thank you, 
Ali 
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Given the centres of the cells you could look at the cumulative distribution of the distances between all pairs of cells.
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Besides Promega, is furimazine, the substrate for Nano Luciferase, available from other sources? I found Promega sells it in kits, which is expensive.
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According to Inouye et al, 2015 (http://dx.doi.org/10.1016/j.pep.2015.02.002), the coelenerazine-h is also a very good substrate for NanoLuc/NanoKAZ.
Although, I didn't see a direct comparison. Furimazine, probably, has lower background, anyway.
PS. According to Promega, Furimazine gives slightly higher initial bioluminescence and the signal then decays much slower compared to CTZ-h.
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Does anyone have experience staining B cells for confocal imaging? I am trying to image B cells under confocal for 3 colors. In the past I tried IgM and IgD and the images did not turn out very well. What surface markers/colors do you recommend, and at what antibody concentrations? Also what do you recommend fixing with? 
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Dear Dan: If you are working on mature B cells; CD19;  B220 are good markers (both for human and mice). Percp is very easy to be bleached under focus, never try this fluorochrome; FITC, PE and APC are good for FACS, but not ideal for Confocal; tandom Abs (say, PE-Cy5) is a bit more stable; but my favourite is alexa fluro confugated Abs which are very tolerant.
Good luck
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I have a sequence of 150 phase contrast time lapse images. I want to zoom and make a movie keeping single cell in a video. Has anybody tried in imageJ?
I am able to make and save the video of original file and not of zoomed images. Can anybody suggest wayout?
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Hello Aditya,
it's quite simple, once you open your sequence as a stack, you can select the rectangular region you want to "zoom in",and then select Image->crop. It will crop the area you selected, so then you can just save it as AVI and have your video.
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I'm doing an invadopodia assay, and from what I found on the literature, people use x63 magnification of the confocal microscope to find a specific area, image it and use ImageJ to analyse the degradation area over the area covered by cells. But one thing that I found is that x63 when image only cover a very small fraction of the observing field when the software snaps the image. So this makes the quantification quite biased and nonrepresentative in my opinion. 
Do you think I can use the smaller magnification (like x40) to take the image to analyse? I asked some people and they said x smaller than 63 doesn't give enough resolution so the quantification will not be accurate. But I would argue that this applied to the whole image so there shouldnt be any change? And also can ImageJ still distinguish the degradation area from the surrounding with lower magnification than 63?
Thank you very much
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OK no, you don't need to calibrate. Your image is calibrated since you have µm mentioned in your image header.
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Hi,
Attached is a sample picture of Leishmania parasites that are stained with mitotracker. This dye gets accumulated into the mitochondria in a potential dependent manner. So, accumulation of the dye in the mitochondria is a measure of the mitochondrial membrane potential. Each parasite has a single mitochondrion which is pretty big in size compared to other eukaryotes. I have such images for wild type parasites as well as from different mutants and I am interested to see if there is any difference in fluorescence intensity. 
Particularly, I would like to use ImageJ for this puropose. However, I am confused about some technical aspects. I would feel great if anybody could explain those to me!
So, my plan is to measure the fluorescence intensity from individual cells and then take the average of them. As the size of the mitochondria may vary cell to cell, how would I maintain the same area of interest across different cells? Is it necessary to maintain the same area or for each cell I will have to draw the line around it's own mitochondrion?
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Dear Sumit,
I have few other suggestions:
1) I think that one key important thing is that the acquisition parameters are the same across the images. I know that is an obvious point, but I saw so many people measuring and comparing fluorescence from image acquired with completely different parameters.
2) Be sure you are not saturating the pixels on your CCD, otherwise you will lose power in your quantification. It does not seems the case in the sample image you posted, but I thought it was worth to mention.
finally for the quantification... I think that the answer on your question depends on what you would like to quantify.
1) The answer above are all valid, however, personally I would stay away from normalisation, Adam is correct in saying that there is variation between coverslips and samples, but I usually deal with this variability making (when possible) more sample for each condition and averaging them across.
2) another point to consider is if you are interested in the total amount of fluorescence, I mean a bigger mitocondrium with the same amount of marker will have a lower mean intensity... You can use the total (or integrated) fluorescence intensity but in this case you have to be careful and remove the background, (a bigger object have a bigger integrated background).
Hope this help,
good luck
Max
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So basically you have a coverslip on a microscope slide and you want to make an unbiased observation of certain representative areas of the coverslip, so that you can later generalise the result to the whole coverslip (similar to random sampling from a population). I know one way to do it is to image 5 photos in an X manner, so 4 images at 4 corners and 1 at the the centre. Data from each image can later be used to generalise to the whole coverslip.
But I'm wondering is there any other method to do this?
Also, sometimes the cells just clump together or distributed unevenly which make this X method a bit inaccurate. Is there any way to troubleshoot this apart from evenly seeding your cells next time? 
Thank you very much
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I always randomly select regions on my coverslip for imaging - to avoid biasing, you can refrain from looking down onto the coverslip while you move in the XY plane. You can do the corners and centre but as your cells clump in middle it's not a good representation.
Just as a matter of interest, when you seed your coverslips with cells, do you swirl the cell mix or do you rock the cell mix once it's in the tissue culture dish/plate? Normally one should not swirl the mix as it causes a vortex in the medium thereby pulling all the cells to the centre of the plate - resulting in uneven distribution and clumping. If you gently rock from left to right, up and down it should give a better distribution. Also preparing the cell mix prior to addition to coverslips is better than having coverslips in fresh medium and adding a small volume of concentrated cells directly to it.
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What is the simple method to calculate FP value with parallel and perpendicular intensities? Any one using Cytation 3 for FP experiment?
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Thanks 
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BioSig3D is a 3D cell image segmentation software that was recently developed at Lawrence Berkeley National Lab., and runs using a Virtual Machine. I've got the VM working, but to upload images for analysis, there's a Java based Image Transfer app. My Java Console blocks the app since it's linked to an http rather than an https site, and using the exceptions list doesn't help either. I was wondering whether anyone else here had managed to get the software working.  
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MATLAB
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I need to collect GFP labelled cells using micromanipulator but cannot see capillary tube for cell collection under fluroscent light. Is there anyway to coat the tip of capillary with some dye to make it visible even under fluorescent lamp in order to facilitate collection. 
Thanks in Advance!
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Try to use phase contrast to see and move a tip of your capillary to the cells. Switch to fluorescence regime just for a short time to catch it. Algorithm: 1) find some cell in fluorescence and keep in mind this area in the view, 2) switch to phase contrast, 3) move a capillary tip close to this cell, 4) switch to fluorescence again (to be sure if this "right" cell) and 5) collect this cell. Such approach may work for small amount of cells...
Probably, a better option is collecting the cells under combined low-intensity phase contrast and fluorescence microscopy.
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I am working on in vitro co-culture intestinal models, and when I try to seed Caco-2 and HT29-MTX cells, I observe changes in the cell surface morphology of HT29-MTX cells. They appear like holes on the surface of the cells when observed with Confocal microscopy (image attached). I have tried monocultures already to confirm that the problem is with HT29-MTX cells and not with Caco-2 cells. I have already tested multiple batches of HT29-MTX, and multiple batches of media, but these problems just continue. Thanks in advance for any help and suggestions. 
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Dear Neha,
You are right. However, that factor of predictability on when such morphological changes will begin to appear is quite difficult to have. Even minor things trigger changes. Let's hope you can resolve these issues with developing fresh cultures from new cell lines.
Regards, Sourav