Just from reading your description, my (WA)guess is you're looking for something like this:

#!/usr/bin/perl

# https://perlmonks.org/?node_id=1223702

use strict;
use warnings;

my @binimage = ( "\x00", "\x00", "\x00", "\x00", "\x00", "\x90" );

my $matrix = join "\n", map({ unpack 'B*', $_ } reverse @binimage), ''
+;

my $transform = ''; # transpose matrix
$transform .= "\n" while $matrix =~ s/^./ $transform .= $&; '' /gem;
print "$transform\n"; # debug print to validate transpose

my $output = pack 'B*', $transform =~ tr/\n//dr; # remove \n, convert 
+to bits

printf "output = %v08B\n", $output;
[download]

Outputs

100000
000000
000000
100000
000000
000000
000000
000000

output = 10000000.00000000.00100000.00000000.00000000.00000000
[download]