What freeware would you recommend for tracing neurons in a tiff stack?

09 September 2018 1 8K Report

I've acquired a stack of tiff images from a volume of brain tissue. I'm trying to find an automated program (not semiautomated) which will allow me to trace the neurites within this volume.

Anton Fomenko

Logan Collins ImageJ has many plugins available both for semi-automated and fully automated neurite tracing. One example of a fully automated plugin can be downloaded here: http://fournierlab.mcgill.ca/styled-6/NeuriteTracer.html

Badges
Science topic

More Logan Collins's questions See All

Does linking alkenes onto tissue increase OsO4 staining density?

I'm trying to increase the contrast of OsO4 stained brain tissue for x-ray microtomography (a recent scan had very poor contrast). I was wondering if there is any literature precedent for getting...

31 December 2019 9,834 1 View

Does EDC/NHS coupling act on primary amides or only primary amines?

I want to use a coupling reagent (possibly EDC/NHS) to link gold nanoparticles to primary amines and NOT primary amides. There are both primary amines and primary amides in my sample, but I want...

31 December 2019 6,329 4 View

How permeable are expanded tissues (when performing expansion microscopy)?

I am planning on performing expansion microscopy on relatively thick (300 um) tissue slices and doing a post-expansion stain with some nanoparticles. It seems that the expansion process should...

31 December 2019 3,550 2 View

How do I store 1% osmium tetroxide [SAFETY QUESTION]?

I'm currently storing a solution of 1% osmium tetroxide (1 gram OsO4 in 100 mL dH2O) in a glass bottle with a plastic cap under a fume hood at room temperature. However, I am concerned that the...

10 November 2019 5,400 15 View

Are there any plastic embedding chemistries that are compatible with very wet tissue?

I'm working with expansion microscopy and I need my samples to have high stability (esp. thermostability) due to intense light beams that are involved in my application. As such, I am trying to...

09 October 2019 7,178 4 View

What are some proteins found on neuronal membranes that are easily amenable to IHC?

I'm looking for a membrane protein (found in neurons) or other antigen that will provide very strong staining from IHC. I would prefer an antigen that is uniformly expressed across dendritic,...

05 June 2019 8,532 7 View

How to make PFA-fixed tissue volumes permeable to nanoparticle-antibody conjugates?

I'm trying to stain ~ 1 mm^3 volumes of PFA-fixed brain tissue with nanoparticle-antibody conjugates. Although my nanoparticles are 5 nm in diameter, I'm experiencing difficulty in getting the...

01 February 2019 5,806 2 View

Where can I find antibodies against cell-surface biomarkers in honeybee neurons?

I'd like to tag honeybee neurons with antibodies for imaging purposes, so I'm looking for a commercial provider of antibodies which are reactive with cell-surface biomarkers found in the honeybee...

09 October 2018 9,103 0 View

What is the "pore size" of brain tissue?

I was wondering about the ECM "pore size" within rat brains (in the context of nanoparticle diffusion). In addition, I would like to know if the fixation/treatment method impacts the tissue's...

05 June 2018 475 9 View

How can I measure MMP-1 protein activity or protein level from liver tissue?

Instead of checking only the mRNA level, I want to check the active protein level of MMP-1 in Liver tissue from mice. How can I do that?

03 March 2021 1,763 2 View

Anyone plz suggest relevant topic for research in image processing+Deep learning.?

I have selected brain tumor images ...but now found that already lots of research done n this topic.

03 March 2021 5,774 3 View

Does any one know how i can prepare liver tissue with transmission electron microscope with good fixation?

i have problem in preparation of liver tissue with bad cell organelles and how i can adjust osmolarity

03 March 2021 8,890 1 View

What kind of food stuff increase the potentiality of human brain?

There are different kinds of food stuffs which we intake daily according to our requirements. Carbohydrate, protein, fat, mineral, vitamin, water are mainly working for the growth and development...

01 March 2021 831 2 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Interested to stain mice tissue with WGA 488 conjugate, anybody has a protocol to recommend?

Interested to stain mice brain tissue with WGA 488 conjugate, appreciate if anyone willing to offer me some guidance or suggestions! Thank you!

28 February 2021 3,951 2 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

B-mercaptoethanol (BME) protocol?

Hi everybody, I have been running a multiplex IHC which allow me to stain the same tissue with different markers (Primary Ab + Secondary conjugated Ab) (AF487, AF555, AF647). Since I would like to...

27 February 2021 5,028 2 View

Can Ethovision store the generated data and video recordings directly to NAS system?

The size of data generated by Ethovision is huge. Having NAS system for data storage seems to be a good option, I am wondering whether Ethovision can directly store the data to the NAS system...

27 February 2021 6,350 2 View

Looking for genomic DNA extraction kits from mouse tissue (centrifuge-based, not spin-column)?

Hello. I am looking to extract genomic DNA from mouse brain and lungs and I need a kit that is not spin-column based because I need to scale up the solution amounts for 400mg tissue (most cap at...

25 February 2021 155 2 View