Skip to main content

Segment regions from fluorescence images

Project description

FlourSeg provides such and such and so and so. You might find it most useful for tasks involving <x> and also <y>. Typical usage often looks like this:

#!/usr/bin/env python

from fluorseg import liffile
from fluorseg import roifile

lif = liffile.LIFFile(path)

#show the path

#show the metadata xml object

#show the number of images in the file

#show the number of layers in each zstack for each image

#show the first image's, 2nd zstack layer

#show the type first channel of the first image's 2nd z-stack layer - each data array is a numpy ndarray
# they are held in nested lists => [image index][z_stack index]

#plot the second channel of the first image's 1st z-stack layer [image index][z_stack index]
plt.imshow(lif.channel_two_images[0][0], interpolation='nearest')

#get the maximum projection of each images z-stack for each image
max_projs_channel_one = [liffile.max_proj(z_stacks) for z_stacks in lif.channel_one_images]
max_projs_channel_two = [liffile.max_proj(z_stacks) for z_stacks in lif.channel_two_images]

#plot the first max_proj
plt.imshow(max_projs_channel_one[0], interpolation='nearest')

plt.imshow(max_projs_channel_two[0], interpolation='nearest')

#get the region of interest info
roi_info = roifile.ROIFile(roi_zip_path) #roi for series 001 only

#make the mask for the second region of interest - a polygon
mask = make_polygon_mask(roi_info.rois[1], 512, 512)

#make the mask for the 5th region of interest - an ellipse
oval_mask = make_oval_mask(roi_info.rois[4], 512,512)

#just get the volume in a region of interest - masking done for you
series1_mp_c2 = max_projs_channel_two[0]
get_region_volume(series1_mp_c2, roi_info.rois[4])

(Note the double-colon and 4-space indent formatting above.)

Paragraphs are separated by blank lines. Italics, bold, and monospace look like this.

A Section

Lists look like this:

  • First
  • Second. Can be multiple lines but must be indented properly.

A Sub-Section

Numbered lists look like you’d expect:

  1. hi there
  2. must be going

Urls are http://like.this and links can be written like this.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for FluorSeg, version 0.0.26.dev0
Filename, size File type Python version Upload date Hashes
Filename, size FluorSeg-0.0.26.dev0-py3-none-any.whl (11.1 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size FluorSeg-0.0.26.dev0.tar.gz (9.9 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page